Harden began the 2003 season with Midland, and in 2 games, he had a 2–0 record and pitched 13 perfect innings, striking out 17 along the way. He was then promoted to the Triple-A Sacramento River Cats of the Pacific Coast League, where he pitched very well. In 16 games, 14 of which he started, Harden went 9–4 with an ERA of 3.15. Overall, Harden finished with a combined 11–4 record, 2.74 ERA, 107 strikeouts and 35 walks in 102 innings in the Minor leagues during the 2003 season. He was then promoted to the Oakland Athletics in July 2003.