On January 16, 2010, Cunningham and Scott Hairston were traded to the San Diego Padres for Kevin Kouzmanoff and Eric Sogard.

[3] In Cunningham's first start as a Padres player on June 15 he hit a grand slam to center field in his first at bat.

While in the majors, he served as a reserve corner outfielder, starting 30 games and hitting a career high .288 in 132 at-bats.

In 2011, Cunningham again split time between the minors and majors, making 20 starts with the Padres at the corner outfield positions.

On July 24 he laid down a successful suicide squeeze bunt to score the winning run in a game against Detroit.