Other athletes photographed include Kaepernick's 49ers teammate, tight end Vernon Davis; John Wall and Kenneth Faried from the NBA; Matt Harvey and Giancarlo Stanton from Major League Baseball; tennis stars Agnieszka Radwanska and John Isner; and soccer player Sydney Leroux.
The fifth annual "Body Issue" hits newsstands July 12.
Player becomes the oldest athlete to appear. Walsh Jennings was shot before and after her daughter was born in April.
ESPN The Magazine editor in chief Chad Milliman says the athletes are "proud of the work they put into being strong and powerful and we're proud that they trust us to capture that."