James Anthony Loney was born on May 7, 1984 in Houston, Texas, to Marion, known as Tony, and Annie Loney. His father was a computer programmer and software consultant and his mother worked as a teacher. Loney has a younger brother named Anthony.

Loney played baseball on a team sponsored by the Reviving Baseball in Inner Cities program and was coached at Elkins High School by Matt Carpenter's father Rick. In Loney's senior year, his high school team was ranked first in the nation by Baseball America and won the 5A state championship. Loney contributed a 12–1 record with a 1.52 ERA and 120 strikeouts as a pitcher that season, as well as a .500 batting average, eight home runs, 38 runs scored and 58 runs batted in. He was named to the Texas Sports Writers Association 5A all-state team at the end of the 2002 baseball season, as well as Powerade and Gatorade Player of the Year.

Much of the professional interest in Loney centered on his pitching ability, but he was drafted by the Los Angeles Dodgers in the first round, #19 overall, of the 2002 Major League Baseball draft as a position player. He had signed with Baylor University to play college baseball, but opted to sign a pro contract.

Loney began his professional career with the Great Falls Dodgers, where he hit .371 and was named the top prospect in the Pioneer League by Baseball America. Loney appeared in 125 games for Single-A Vero Beach in 2003 and hit .276 with 7 homers and 46 RBIs. He was listed #34 on the 2003 edition of Baseball America's Top 100 Prospects list.

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