Headley hit .305 with 79 hits in 259 at-bats with the Portland Beavers. He collected 24 doubles, one triple, 13 homers, 49 runs scored, and 40 RBIs. He also drew 31 walks compared to 65 strikeouts for a .383 on-base percentage.

Headley hit .269 with 89 hits in 331 at-bats with the San Diego Padres. He collected 19 doubles, two triples, nine homers, 34 runs scored, and 38 RBIs across 91 games. He also drew 30 walks compared to 104 strikeouts for a .337 on-base percentage and stole four bases in five attempts.

2007

Headley was named the Texas League Player of the Year and a postseason All-Star.

Headley hit .269 with two homers, four RBIs and five runs scored over seven Missions playoff games.

2006

Headley also played in the Arizona Fall League.

Chase Headley was selected to play in the California League All-Star game in 2006, representing the Lake Elsinore Storm.

He was also named to the 2006 California League Post-Season All-Star Team, the only member of the team to be so honored.

Headley hit .291 with 141 hits in 484 at bats over 129 games with the Lake Elsinore Storm. He had 33 doubles, 12 homers, scored 79 runs, and added 73 RBI's. He also drew 74 walks and whiffed 96 times.

2005

Headley was selected by the Padres in the second round of the 2005 MLB Draft.

In 57 games with Eugene, Headley hit .268 with a team-high 14 doubles, six home runs and 33 RBI. He was promoted to the Fort Wayne Wizards on August 31, 2005.

Headley went 3-for-15 in four games with Fort Wayne to end the year.