Hill was selected in the fourth round of the 2002 Major League Baseball draft by the Chicago Cubs and signed on July 10, 2002. He had been rated as having one of the best curveballs in the draft but mechanical and control issues kept him out of the early rounds. He began his professional career with the Boise Hawks of the Northwest League, where he was 0–2 with an 8.36 ERA in six games. In 2003 with Boise he was 1–6 with a 4.35 ERA in 14 starts and led the Northwest League in strikeouts with 99. He was promoted to the Lansing Lugnuts of the Midwest League, where he was 0–1 with a 2.76 ERA in 15 games (4 starts).