Following the 2008 season, he was claimed off waivers by the Brewers, and added to the Brewers' 40-man roster.
Originally slated for a utility role in 2009, McGehee found himself playing at third base after Bill Hall struggling at the place and Mat Gamel struggled at defense. After hitting his first home run on June 14, 2009 off of Mark Buehrle of the Chicago White Sox, McGehee hit his way into the starting lineup with a .368 average and five homers over 76 at-bats in June. He cooled off in July and August, but finished strong with a .337 mark and five more homers in September. After playing in 116 games, McGehee finished his rookie season with a .301 batting average with 16 home runs and led all Major League rookies with 66 RBIs, playing the whole season on a bum knee.
McGehee finished fifth in National League Rookie of the Year balloting, receiving one first-place vote, three second-place votes and four third-place votes from members of the Baseball Writers' Association of America for 18 total points, based on a 5-3-1 tabulation system. He was bidding to be the Brewers' second rookie winner in three years. Ryan Braun won in 2007, the first Brewer to win the honor since Pat Listach in 1992. Florida Marlins outfielder Chris Coghlan won the award, leading NL rookies in batting average (.321), runs (84), hits (162), doubles (31), total bases (232), multi-hit games (51) and on-base percentage (.390).