©2016 PATHEON®

4Q/FY 2016

Financial Results

Call

December 2016

2 | ©2016 PATHEON®

Forward-Looking Statements

This presentation contains forward-looking statements which reflect the current beliefs and expectations of

Patheon’s management regarding the company’s future growth, results of operations, performance (both operational

and financial) and business prospects and opportunities. The statements in this presentation are not historical facts

and may be forward-looking statements. Readers can identify these forward-looking statements by the use of words

such as ‘‘outlook,’’ ‘‘believes,’’ ‘‘expects,’’ ‘‘potential,’’ ‘‘continues,’’ ‘‘may,’’ ‘‘will,’’ ‘‘should,’’ ‘‘seeks,’’ ‘‘approximately,’’

‘‘predicts,’’ ‘‘intends,’’ ‘‘plans,’’ ‘‘estimates,’’ ‘‘anticipates’’ or the negative version of these words or other comparable

words. Such forward looking statements are subject to various risks and uncertainties, which could cause actual

results to differ from those indicated in these forward looking statements. For more information concerning factors

that could cause actual results to differ materially from those conveyed in the forward-looking statements, please

refer to the "Risk Factors" section of the prospectus included in the company’s registration statement, in the form last

filed with the SEC. The Company undertakes no obligation to publicly update or review any forward-looking

statement, whether as a result of new information, future developments or otherwise, except as required by

applicable law. Accordingly, readers should not place undue reliance on forward-looking statements as a prediction

of actual results.

Use of Non-GAAP Financial Measures

See the Appendix for additional information regarding the use of Non-GAAP financial measures.

FORWARD-LOOKING STATEMENTS AND NON-GAAP MEASURES

3 | ©2016 PATHEON®

Growth across all segments, helping clients simplify the supply chain

Strong financial performance in the quarter and for the year

Positive momentum going into 2017, 85% of next year’s revenue locked in

Execute on the M&A strategy - acquisition of North American API site

Invest in new capabilities to support key growth areas – sterile and Biologics

Outlook for 2017 in line with consensus of analyst’s estimates

STRONG 2016 PERFORMANCE – POSITIVE MOMENTUM INTO 2017

4 | ©2016 PATHEON®

STRONG Q4 FINANCIAL RESULTS

STRONG GROWTH DELIVERS 24% ADJUSTED EBITDA MARGIN

REVENUE ($M)

ADJUSTED EBITDA ($M) KEY CONSIDERATIONS

10% Growth

4Q16 4Q15

17% Growth

4Q16 4Q15

• Shares Outstanding Q4’16: 145M

• Diluted Weighted Avg. Shares Q4’16: 146M

• Interest Expense Q4’16: $31M, including ~$3M amortization of

deferred financing costs

• Q4’16 adjusted EPS positively impacted by favorable tax expense

$462 $510

$106

$124

ADJUSTED NET INCOME ($M)

22% Growth

4Q16 4Q15

$55

$67

Adj. EPS

$0.46

5 | ©2016 PATHEON®

Revenue up 10% y/y to $298 million

Adj. EBITDA up 14% y/y to $80 million

Adj. EBITDA margin 27%

• Continued volume growth and demand

across sterile and oral solid dose

• Key client wins

• 2017: ~95% of revenue under contract

Revenue up 18% y/y to $60 million

Adj. EBITDA up 36% y/y to $23 million

Adj. EBITDA margin 37%

• Strong demand for sterile and low-

solubility services

• Improved productivity across the

network

• 2017: ~ 45% of revenue under

contract

Q4’16: BROAD-BASED GROWTH ACROSS ALL SEGMENTS

PHARMACEUTICAL DEVELOPMENT

SERVICES (PDS)

Revenue up 10% y/y to $152 million

Adj. EBITDA up 9% y/y to $49 million

Adj. EBITDA margin 32%

• Continued strong demand for biologic

services

• Biologics represents approximately

50% of the segments revenues

• 2017: ~85% of revenue under contract

DRUG PRODUCT

SERVICES (DPS)

DRUG SUBSTANCE

SERVICES (DSS)

6 | ©2016 PATHEON®

CASH POSITION OF $165 MILLION

Delevering

5.6x*

4.7x*

Q4FY16

LTM

Q4FY15

LTM

• Deleverage rapidly through debt reduction

and Adjusted EBITDA expansion

Cash Position

Q4: $347M total liquidity

• *Leverage ratios derived using total debt on the balance sheet less cash on the balance sheet divided by LTM pro-forma

Adjusted EBITDA

• ** NTM Leverage based on forecasted Adjusted EBITDA

Refer to reconciliation tables for LTM pro-forma adjusted EBITDA

• *** Net of cash used for debt repayment in Q4

$2.1B Gross Debt

$2.0B Net Debt

* Incl. $20M borrowing from revolver facility

• NTM Leverage Ratio = 4.1x**

Leverage ratio is calculated based on net debt and pro forma adjusted EBITDA

Cash Position:

Q3: $100 million****

Q4: $165 million*

7 | ©2016 PATHEON®

CONTINUED GROWTH WITH STRONG MOMENTUM

Growth across all 3 segments

Strong demand for services

Successful IPO; reducing leverage

SIGNIFICANT ACHIEVEMENTS

• Successful IPO

• Key management additions: new President,

leaders in API and Biologics segments

• Added high-quality API capacity with facility

acquisition

SOLID BUSINESS MOMENTUM

• More than 100 Tech Transfers in 2016

• More than 50 Launches

o 17 New Drug Approvals in FY 2016

• 470 New Contracts Including:

o Boehringer Ingelheim, Amgen, Grünenthal

• Positive strategic dialogues with clients

8 | ©2016 PATHEON®

ACQUISITION OF STATE OF THE ART API FACILITY EXPECTED TO CLOSE FEBRUARY 2017

Florence, South Carolina STRONG BENEFITS

Expanded API capacity in North America

Margin Enhancement Opportunities

Immediate Capacity Utilization

Long-Term Growth

SIGNIFICANT OPPORTUNITY

State of the art facility

200 professionals, 1,100 acre site to support continued growth

Multi-year manufacturing agreement with Roche

CONFIDENTIAL ©2016 PATHEON®

FY 2017

OUTLOOK

©2016 PATHEON® 10 |

2014 2011 2012 2013 2015

4% Adj. EBITDA Margin

12% 21% 17% 14%

OUTPACING MARKET GROWTH ON BOTH THE TOP LINE AND BOTTOM LINE

SOLID TRACK RECORD OF PERFORMANCE

395248

1438729

1,867

991

748648

1,774

1,484

375

Adjusted EBITDA*

Revenue

$ in millions

**

**

*Non-GAAP, see Appendix for reconciliation.

**Adjusted for contract termination fee.

*** CAGR for 2013-2015 and includes FX adjustments

2016

21%

8% CAGR***

Organic Growth

Revenue from

5 Acquisitions

in 5 Years

(excluding divestitures)

$700M

©2016 PATHEON® 11 |

FY17 GUIDANCE | OVERVIEW

Mid-term Financial Objectives at IPO

ORGANIC REVENUE

GROWTH OF 8-9%

SOLID MARGIN PROFILE

~150 bps expansion per annum

ORGANIC REVENUE

GROWTH OF 10%

$2,050M, on a currency neutral

basis

ADJ EBITDA MARGIN

EXPANSION OF 200bps

Adj. EBITDA of $475M

FY 2017 Outlook

©2016 PATHEON® 12 |

FLORENCE SITE

ACQUISITION NOT

INCLUDED

KEY ASSUMPTIONS FOR FY 2017 OUTLOOK

REVENUE GROWTH OF 10% ASSUMES:

INTEREST EXPENSE:

$108M

Excluding amortization of

deferred financing costs

PATHEON-FUNDED

CAPEX:

$155M

2/3 growth CapEx

CURRENCY NEUTRAL

The avg rate of 2016 Euro / US

of $1.11

EVERY $0.01 RATE

CHANGE

CURRENCY

COMPOSITION:

ADDITIONAL ITEMS

Impacts top line by $5M and

Adj EBITDA by $1M

65% Dollar/ 30% Euro/

5% Other

2017 US revenue outlook

would be $2,070M

AT EURO/US $1.15

RATE AT IPO

HIGH VISIBILITY TO

FY17 BUSINESS

DEMANDS:

85% of FY17 revenue locked in

13 | ©2016 PATHEON®

2017 ADJ. EBITDA, ADJ. NET INCOME AND ADJ. EPS

Adjusted Net Income: $202 - $222

~147M Shares

Adjusted EPS

$1.37 - $1.51

Based on 2017 FactSet Consensus Estimate of Analysts

$40 - $60

$108

$105

$202 - $222

$475

Adjusted

EBITDA Depreciation Interest

Expense Tax

Impacts Adjusted Net

Income

14 | ©2016 PATHEON®

LEADING INDICATOR OF LONG-TERM TOTAL CONTRACT VALUE (TCV)

• Metric built on historical analysis of Patheon sales to revenue conversion rates

• Signed business only

• Indicator of long-term growth

• TCV naturally ramps throughout fiscal year

• Combined with base business, supports 8-9% revenue growth

• Long and Short Conversion Cycles

o 12 to 24 months for commercial

o 6 to 18 months for development

• High forward visibility, sticky revenue

streams

• Avg. Length of Contract

o Commercial - 5 to 10 years

o Development - 18 to 24 months

TCV = revenue expected to be booked over the life of the

contracts closed in the current year

15 | ©2016 PATHEON®

2021-2025 2017 2018 2019 2020

Total Contract Value

Development

Commercial

$2.0 – 2.2B

FY17

New

Business

Wins

Revenue

Conversion

TOTAL CONTRACT VALUE OF $2B+ IN 2017 EXAMPLE OF SALES TO REVENUE CONVERSION

TCV = Revenue expected to be booked over the life of the contracts closed in the current year

ILLUSTRATIVE

16 | ©2016 PATHEON®

DRIVING ABOVE-MARKET PERFORMANCE

STRONG CLIENT

DEMAND

ABOVE-MARKET

REVENUE GROWTH

SOLID MARGIN

PROFILE

CONFIDENTIAL ©2016 PATHEON®

Questions?

18 | ©2016 PATHEON®

RECONCILIATION OF GAAP TO NON-GAAP MEASURES Unaudited

Three months ended Three months ended Twelve months ended Twelve months ended

10/31/2016 10/31/2015 10/31/2016 10/31/2015

(in millions of U.S. dollars, except share data) $ $ $ $

Net income from continuing operations $ 44.1 $ 40.8 $ 34.8 $ 34.9

Depreciation and amortization 31.5 28.5 113.0 107.8

Repositioning expenses 6.3 3.8 9.2 25.1

Acquisition and integration costs 4.0 4.0 16.6 22.3

Interest expense, net 30.9 42.8 160.4 141.8

Impairment charge - 0.9 - 4.1

(Benefit from) provision for income taxes (24.3) (19.5) (24.0) 0.3

Refinancing expenses 21.6 - 21.6 3.7

Operational initiatives related consulting costs 0.3 4.1 4.2 13.0

IPO costs 0.9 2.1 2.0 4.5

Acquisition-related litigation expenses 1.0 4.9 4.0 12.7

Stock-based compensation expense 5.3 2.6 21.6 13.9

Remediation costs 5.3 2.6 32.8 2.6

Gain on sale of third party investment - (16.2) - (16.2)

Other (3.0) 4.7 (1.6) 4.1

Total Adjusted EBITDA $ 123.9 $ 106.1 $ 394.6 $ 374.6

Depreciation (25.2) (23.7) (88.4) (85.1)

Interest expense (28.2) (39.6) (147.8) (130.6)

Tax expense 24.3 19.5 24.0 (0.3)

Discrete tax items (20.2) (5.1) (29.0) (6.0)

Estimated tax effect on adjustments (7.2) (1.9) (26.5) (18.2)

Adjusted net income $ 67.4 $ 55.3 $ 126.9 $ 134.4

Weighted average shares - diluted (in millions) 145.8 115.6 124.3 115.6

Adjusted net income per diluted share $ 0.46 $ 0.48 $ 1.02 $ 1.16

19 | ©2016 PATHEON®

CONSOLIDATED SEGMENT OPERATIONS Unaudited

(in millions of U.S. Dollars)

Three months ended October 31, 2016

Revenues Adjusted EBITDA

$ $

DPS 297.9 80.4

PDS 60.4 22.6

DSS 152.2 49.1

Other - (28.2)

Intersegment Eliminations (0.3) -

Total 510.2 123.9

Three months ended October 31, 2015

Revenues Adjusted EBITDA

$ $

DPS 272.4 70.6

PDS 51.2 16.6

DSS 138.5 45.2

Other - (26.3)

Intersegment Eliminations (0.1) -

Total 462.0 106.1

20 | ©2016 PATHEON®

RECONCILIATION FOR CONSOLIDATED EBITDA per CREDIT AGREEMENT Unaudited

Twelve Months

Ended October 31,

2016

(in millions of U.S. dollars) $

Consolidated EBITDA per Credit Agreement 420.2

Less

Pro forma cost savings (24.8)

Other (0.8)

Adjusted EBITDA 394.6

(Deduct) add

Depreciation and amortization (113.0)

Repositioning expenses (9.2)

Acquisition and integration costs (16.6)

Interest expense, net (160.4)

Benefit from income taxes 24.0

Refinancing expenses (21.6)

Operational initiatives related consulting costs (4.2)

IPO Costs (2.0)

Acquisition-related litigation expenses (4.0)

Stock-based compensation expense (21.6)

Remediation costs (32.8)

Other 1.6

Income from continuing Operations 34.8

Add (deduct):

Depreciation and amortization 113.0

Stock-based compensation expense 21.6

Net change in non-cash working capital (175.9)

Net change in deferred revenues 92.7

Non-cash interest 25.3

Other, primarily changes in long-term assets and liabilities of deferred taxes (50.7)

Cash flows from operating activities of continuing operations 60.8

Cash flows from operating activities of discontinued operations (2.9)

Cash flows from operating activities 57.9

Cash flows from investing activities (206.7)

Cash flows from financing activities (16.0)

21 | ©2016 PATHEON®

ADJUSTED EBITDA RECONCILIATION Unaudited

FY 2011 FY 2012 FY 2013 FY 2014 FY 2015 FY 2016

(in millions of U.S. dollars) $ $ $ $ $ $

Net (loss) income from continuing operations (16.1) (106.7) (32.6) (117.1) 34.9 34.8

Depreciation and amortization 53.2 40.8 46.9 79.5 107.8 113.0

Repositioning expenses 7.0 6.1 15.8 51.7 25.1 9.2

Acquisition and integration costs - 3.2 17.0 60.3 22.3 16.6

Interest expense, net 25.6 26.5 47.9 90.5 141.8 160.4

Impairment charge - 57.9 13.1 9.7 4.1 -

Provision for (benefit from) income taxes 1.1 43.4 (3.7) 4.3 0.3 (24.0)

Refinancing expenses - - 27.3 28.2 3.7 21.6

Operational initiatives related consulting costs 9.0 13.3 2.3 10.1 13.0 4.2

IPO costs - - - - 4.5 2.0

Acquisition-related litigation expenses - - 6.4 10.2 12.7 4.0

Stock-based compensation expense 3.5 3.1 3.2 10.0 13.9 21.6

Remediation costs - - - - 2.6 32.8

Purchase accounting adjustments - - 2.8 11.4 -

Gain on sale of third party investment - - - - (16.2) -

Other (4.7) (0.5) (3.6) (0.5) 4.1 (1.6)

Total Adjusted EBITDA 78.6 87.1 142.8 248.3 374.6 394.6

22 | ©2016 PATHEON®

2011 REVENUE AND ADJUSTED EBITDA RECONCILIATION

($ in millions) Revenue Adjusted EBITDA

2011 Reported 698.0 78.6

Contract cancellation fee 50.0 50.0

Pro forma results 648.0 28.6

23 | ©2016 PATHEON®

Use of Non-GAAP Financial Measures

We define Adjusted EBITDA as income (loss) from continuing operations before repositioning expenses (including certain product returns and inventory write-offs

recorded in gross profit), interest expense, foreign exchange losses reclassified from other comprehensive income (loss), refinancing expenses, acquisition and

integration costs (including certain product returns and inventory write-offs recorded in gross profit), gains and losses on sale of capital assets, Biologics earnout income

and expense, income taxes, impairment charges, remediation costs, depreciation and amortization, stock-based compensation expense, consulting costs related to our

operational initiatives, purchase accounting adjustments, acquisition-related litigation expenses and other income and expenses.

We define Adjusted net income as Adjusted EBITDA minus depreciation expense (excluding amortization from intangibles acquired in acquisitions), interest expense

(excluding amortization of the deferred financing costs), and tax expense. In addition, we exclude discrete tax items and apply an estimated tax effect on adjustments

within the calculation. The estimated tax effect is calculated using statutory tax rates on each expense item, except in the case where a jurisdiction is under a full valuation

allowance at the time of the expense, in which we apply a tax rate of 0%. We define Adjusted EPS as Adjusted net income divided by the average number of shares

outstanding on a diluted basis for the related period.

Our management uses Adjusted EBITDA as one of several metrics to measure the Company’s operating performance. Adjusted EBITDA is also a component of the

performance objectives used to determine the short and long-term incentive portions of executive compensation. We present Adjusted net income and Adjusted EPS

because we believe they are useful supplemental measures in evaluating the performance of our operations and provide greater transparency into our results. We believe

that providing these non-GAAP financial measures to investors as a supplement to the comparable U.S. GAAP measures in evaluating the performance of our operations

provides greater transparency to the information used by the Company’s management in its financial and operational decision-making. These non-GAAP financial

measures do not have standard meanings, so they may not be comparable to similarly-titled measures presented by other companies and should not be considered in

isolation or as a substitute for U.S. GAAP financial measures of performance. Reconciliation of Adjusted EBITDA to the most comparable U.S. GAAP financial measure is

included with the financial statements in this press release.

The Company does not provide a reconciliation of forward-looking non-GAAP financial measures to their comparable GAAP financial measures because it could not do so

without unreasonable effort due to the unavailability of the information needed to calculate reconciling items and the variability, complexity and limited visibility of the

adjusting items that would be excluded from the non-GAAP financial measures in future periods. When planning, forecasting and analyzing future periods, the Company

does so primarily on a non-GAAP basis without preparing a GAAP analysis as that would require estimates for various cash and non-cash reconciling items that would be

difficult to predict with reasonable accuracy. For example, equity compensation expense would be difficult to estimate because it depends on the Company’s future hiring

and retention needs, as well as the future fair market value of the Company’s common stock, all of which are difficult to predict and subject to constant change. It is

equally difficult to anticipate the need for or magnitude of a presently unforeseen one-time restructuring expense or the values of end-of-period foreign currency exchange

rates. As a result, the Company does not believe that a GAAP reconciliation to forward-looking on-GAAP financial measures would provide meaningful supplemental

information about the Company’s outlook.

USE OF NON-GAAP FINANCIAL MEASURES