On November 5, 2013, fourteen minor leaguers in the Padres organization were granted free agency. Of those fourteen, four have signed on with a new team.
- Third baseman Scott Moore signed with the Cardinals on November 11. Moore, who spent parts of five years in the majors with the Cubs, Orioles, and Astros, hit .260/ .336/ .382 with three homers in 39 games with the Padres' AAA affiliate, the now-defunct Tucson Padres last season.
- Tucson outfielder Brandon Allen signed with the Mets on November 19. Allen played 116 games in the bigs with Arizona, Oakland, and Tampa Bay from 2009 through 2012. He slashed .267/ .347/ .478 with 24 doubles and 17 homers in 423 at-bats over 119 games with the TuPads. The 2014 season will be his eleventh in the minors.
- Left-handed reliever Tommy Layne inked a deal with the Red Sox on November 10. Layne had a 2-2 record with a 2.84 ERA in 40 games as a LOOGY for the Padres in 2012 and 2013. He hasn't been as successful in AAA, posting a 6.40 ERA in 209.2 innings spread over 91 games in three seasons split between Tucson and the Diamondbacks' affiliate in Reno.
- Right-handed outfielder Mike Wilson signed with the Reds organization on November 6. Wilson, whose major league experience consists of four hits in 27 at-bats with the 2011 Mariners, saw action in 76 games with Tucson last year. He batted .291 with 13 doubles and seven homers in 220 at-bats.
The ten players who have yet to sign with anyone are Eddie Bonine, Fautino De Los Santos, Dan Cortes, Josh Geer, Clay Zavada, Chris Robinson, Eddy Rodriguez, Gregorio Petit, Travis Buck, and Ben Francisco.
In addition to the players listed above, another Padres minor leaguer has signed on with another organization. Right-handed starter Sean O`Sullivan was granted free agency on October 1, and signed with the Phillies on December 18. O`Sullivan went 8-5 with a 3.83 ERA in 20 starts for Tucson in the hitter-friendly Pacific Coast League. He got into seven games with his hometown San Diego Padres, starting three of them, and posted a 3.96 ERA in 25 innings.