Microsoft Thursday announced that Jeff Raikes, president of its business division, would be leaving the company in September and will be replaced by Stephen Elop, the former chief operating officer at Juniper Networks.

The announced departure of Raikes, a 26-year veteran of Microsoft, comes just six months before Bill Gates will step down from his full-time duties at the company. Gates will remain as chairman.

Raikes is the second executives to step down in as many days. Wednesday, Bruce Jaffe, corporate vice president in charge of mergers and acquisitions, said he will leave the company at the end of February. Jaffe last year presided over Microsoft’s largest acquisition ever, a $6 billion deal to acquire aQuantive.

Elop will start at Microsoft at the end of January and he and Raikes will work side by side during a nine-month transition. Elop will eventually assume responsibility for the information worker, Microsoft business solutions and unified communications businesses — all previously led by Raikes.

In addition, Microsoft announced that Bob Muglia, senior vice president of the server and tools business, will move to report directly to CEO Steve Ballmer. He will continue to manage server and tools.

For the past two years, Raikes, 49, has been instrumental in pushing the company’s information worker strategy and its VoIP initiative. On Tuesday, he was the executive who announced Microsoft’s $1.23 billion offer to acquire Fast Search & Transfer.

Raikes has been a high-profile executive with Microsoft as part of the company’s senior leadership team that includes Ballmer and Gates.

Prior to September 2005, Raikes was group vice president of the information worker business, which was responsible for the Microsoft Office applications, servers, and software-based services.

He previously served as group vice president of the worldwide sales and support group. Prior to that, Raikes served as senior vice president of Microsoft North America, a position he had held since 1993. He joined Microsoft in 1981 as a product manager and drove Microsoft’s applications marketing strategy.

“Since 1981, I’ve had an incredible journey here at Microsoft. Given the success of our business and the depth of leadership we have in place today, the time is right for me to leave the MBD business in the capable hands of our new generation of leaders,” Raikes said in a statement.

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