The star duo will be joined by US Amateur champion Gunn Yang of South Korea, the group teeing off on the 10th hole at 11:28 am (18:28 GMT) on Thursday.
Kaymer also won the 2010 PGA Championship, while McIlroy is the reigning British Open and PGA Championship winner.
Six-time runner-up Phil Mickelson will play alongside 2007 titlist Angel Cabrera and two-time Masters winner Bubba Watson.
Tiger Woods, whose 14 major titles include three US Opens, will play alongside Rickie Fowler and 2010 Open Champion Louis Oosthuizen of South Africa for the first two rounds.
Former champions Geoff Ogilvy, Ernie Els and Retief Goosen are paired together for the first two days, according to the US Golf Association, which released the pairings for the first two rounds of the year's second major championship.
The Chambers Bay course south of Seattle is hosting the US Open for the first time. McIlroy was to get his first look at it in a practice round on Saturday.
In a nod to local history by the USGA, local resident Michael Putnam, who played in the first group at Chambers Bay when the course opened in 2007, will be the first player off the first tee when the tournament begins on Thursday.
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