Exhibit 99.1

Brooks Automation Reports Fiscal First Quarter Ended December 31, 2012 Results and Timetable for Chief Financial Officer Retirement

CHELMSFORD, Mass., January 31, 2013 Brooks Automation, Inc. (Nasdaq:BRKS), a leading worldwide provider of automation, vacuum and instrumentation solutions for multiple markets, including semiconductor manufacturing and life sciences, today reported financial results for the first quarter ended December 31, 2012.

Fiscal First Quarter 2013 Financial and Operational Highlights:

Summary of GAAP and Non-GAAP Earnings

A reconciliation of non-GAAP measures to the most nearly comparable GAAP measure follows the consolidated statements of operations, balance sheets and statements of cash flows included in this release.

Management Comments

“Consistent with our outlook for the quarter, we experienced a 20% sequential decline in product revenues for front-end semiconductor applications and a 31% sequential decline in revenues into our industrial customers as caution and uncertainty drove weak demand across almost all market sectors we serve. However, our Life Science Systems business increased on both a sequential and year-over-year basis as we continue to win the majority of the market share opportunities for automated sample management systems,” said Steve Schwartz, President and Chief Executive Officer of Brooks. “The integration of Crossing Automation into Brooks is moving ahead effectively and quickly. We are ahead of our aggressive schedule to drive annualized integration synergies of $12 million within the first five quarters of ownership. We are also pleased with the opportunities already opening up for revenue growth in atmospheric automation from developments using both Brooks and Crossing technologies.”

Dr. Schwartz continued, “We see modest improvement in most of our markets in the March 2013 quarter. While near term visibility is limited, we view favorably the capital expenditure plans of end users for our products and consequently expect a far stronger second half to our current fiscal year.”

First Quarter Fiscal 2013 Results

Revenues for the first quarter of fiscal 2013 were $98.0 million, compared to revenues of $119.5 million in the fourth quarter of fiscal 2012 and $120.2 million in the first quarter of fiscal 2012. The revenues for the first quarter of fiscal 2013 included $6.5 million of product sales and $2.0 million of service sales from the acquisition of Crossing Automation that closed one month into the quarter.

Revenues for the Brooks Global Services segment increased 0.3% on a sequential basis compared to the fiscal fourth quarter of 2012 with the addition of Crossing service revenues. Revenues for the Brooks Product Solutions segment declined 26% sequentially due to overall industry weakness. Revenues for the Brooks Life Science Systems segment grew sequentially to $14.1 million compared to the fourth quarter of 2012 at $13.9 million and grew 10% on a year-over-year basis.

Order bookings for the first quarter of fiscal 2013 declined sequentially 5% to $92.6 million, compared to order bookings in the fiscal fourth quarter 2012 of $97.5 million.

Gross profit margin was 29.7% for the first quarter of fiscal 2013, compared to gross profit margins of 32.3% for the fourth quarter of fiscal 2012 and 33.6% for the first quarter of fiscal 2012. Excluding acquisition related nonrecurring charges, gross profit margin was 31.9% for the first quarter of fiscal 2013, compared to gross profit margins of 32.3% for the fourth quarter of fiscal 2012 and 33.9% for the first quarter of fiscal 2012. The first quarter of fiscal 2013 sequential margin improvements in Services and Life Sciences were offset by a decrease in Product Solutions margins off lower revenue volumes.

Adjusted EBITDA (as defined in the Notes on non-GAAP measures) for the first quarter of fiscal 2013 was $3.3 million, which compared to $10.2 million in the fourth quarter of fiscal 2012 and $10.6 million in the first quarter of fiscal 2012.

A reconciliation of non-GAAP measures to the most nearly comparable GAAP measure follows the consolidated statements of operations, balance sheets and statements of cash flows included in this release.

Net cash provided by operating activities for the first quarter of fiscal 2013 was $5.1 million, which resulted in total cash, cash equivalents and marketable securities of $142 million at December 31, 2012.

Quarterly Cash Dividend

The Company additionally announced that the Board of Directors had declared a dividend of $0.08 per share payable on March 29, 2013 to stockholders of record on March 8, 2013. Future dividend declarations, as well as the record and payment dates for such dividends, are subject to the final determination of the Company’s Board of Directors.

Guidance for Second Fiscal Quarter

The Company announced revenue and earnings guidance for the second quarter of fiscal 2013. Revenues are expected to range between $102 and $110 million and non-GAAP earnings per share are expected to range between breakeven and a loss of $(0.05). Including restructuring and acquisition related charges, GAAP adjusted loss per share is expected to be between $(0.03) and $(0.10) per diluted share.

Retirement of Chief Financial Officer

The Company announced that Martin S. Headley, Executive Vice President and Chief Financial Officer has given notice of his intention to retire. The Company and Mr. Headley have agreed in principle to the terms of a retention agreement pursuant to which he would remain in his role through the end of June 2013. The Company will be initiating a search and expects to be able to name a successor within this timeframe.

“It has been my distinct pleasure to have worked closely with Martin over the past three years,” states Dr. Schwartz. “Martin’s extensive financial experience and strategic insight have made him an outstanding partner and business leader as we repositioned the Company. We will miss his leadership and guidance but wish him the best in his retirement.”

“My tenure at Brooks has afforded an opportunity to work with many outstanding people and address unique business challenges and I am extremely proud of what we have accomplished at Brooks over my five plus years as CFO,” stated Mr. Headley. “As I have been considering my future plans over the last several weeks, I have worked closely with Steve and our Board to ensure that we will have a smooth transition.”

Conference Call

Brooks management will webcast its first quarter earnings conference today at 4:30 p.m. Eastern Time to discuss the fiscal first quarter business highlights. During the call, Company management will respond to questions concerning, but not limited to, the Company’s financial performance, business conditions and industry outlook. Their responses could contain information that has not been previously disclosed.

The call will be broadcast live over the Internet hosted at the Investor Relations section of Brooks’ website at www.brooks.com, and will be archived online on this website for convenient on-demand replay. In addition, you may call 1-800-734-8583 (North America only) or 1-212-231-2930 to listen to the live broadcast.

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About Brooks Automation, Inc.

Brooks is a leading worldwide provider of automation, vacuum and instrumentation solutions for multiple markets including semiconductor manufacturing, life sciences, and clean energy. Our technologies, engineering competencies and global service capabilities provide customers speed to market, and ensure high uptime and rapid response, which equate to superior value in their mission-critical controlled environments. Since 1978, we have been a leading partner to the global semiconductor manufacturing market and through product development initiatives and strategic business acquisitions; we have expanded our reach to meet the needs of customers in the life sciences industry, analytical & research markets and clean energy solutions. Brooks is headquartered in Chelmsford, MA, with direct operations in North America, Europe and Asia.

For more information, please visit www.brooks.com.

“Safe Harbor Statement” under Section 21E of the Securities Exchange Act of 1934

Some statements in this release are forward-looking statements made under Section 21E of the Securities Exchange Act of 1934. These statements are neither promises nor guarantees but involve risks and uncertainties, both known and unknown, that could cause Brooks’ financial and business results to differ materially from our expectations. They are based on the facts known to management at the time they are made. These forward-looking statements include statements regarding our revenue and operating margin expectations, our ability to develop further our business in new and adjacent markets, and our ability to achieve financial success in the future. Factors that could cause results to differ from our expectations include the following: volatility of the industries the Company serves, particularly the semiconductor industry; our possible inability to meet demand for our products due to difficulties in obtaining components and materials from our suppliers in required quantities and of required quality; the inability of customers to make payments to us when due; the timing and effectiveness of cost reduction and cost control measures; price competition; disputes concerning intellectual property; continuing uncertainties in global political and economic conditions, and other factors and other risks that we have described in our filings with the Securities and Exchange Commission, including but not limited to our Annual Report on Form 10-K, current reports on Form 8-K and our quarterly reports on Form 10-Q. As a result we can provide no assurance that our future results will not be materially different from those projected. Brooks expressly disclaims any obligation or undertaking to release publicly any updates or revisions to any such statement to reflect any change in our expectations or any change in events, conditions or circumstances on which any such statement is based. Brooks undertakes no obligation to update the information contained in this press release.

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BROOKS AUTOMATION, INC.

CONSOLIDATED BALANCE SHEETS

(unaudited)

(In thousands, except share and per share data)

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BROOKS AUTOMATION, INC.

CONSOLIDATED STATEMENTS OF OPERATIONS

(unaudited)

(In thousands, except per share data)

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BROOKS AUTOMATION, INC.

CONSOLIDATED STATEMENTS OF CASH FLOWS

(unaudited)

(In thousands)

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Notes on Non-GAAP Financial Measures:

The information in this press release is for: internal managerial purposes; when publicly providing guidance on future results; and as a means to evaluate period-to-period comparisons. These financial measures are used in addition to and in conjunction with results presented in accordance with GAAP and should not be relied upon to the exclusion of GAAP financial measures. Management believes these financial measures provide an additional way of viewing aspects of our operations, that, when viewed with our GAAP results and the accompanying reconciliations to the corresponding GAAP financial measures, provide a more complete understanding of our business. Management strongly encourages investors to review our financial statements and publicly-filed reports in their entirety and not rely on any single measure.

The press release includes financial measures which exclude the effects of non-recurring income and special charges such as restructuring charges and acquisition related charges. Management believes these measures are useful to investors because it eliminates accounting charges that do not reflect Brooks’ day-to-day operations. A table reconciling income (loss) and diluted earnings (loss) per share from operations is presented below.

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