June 3, 2003: Tim Stauffer was drafted by the San Diego Padres in the 1st round (4th pick) of the 2003 amateur draft. Player signed August 11, 2003.
June 3, 2003: Dirk Hayhurst was drafted by the San Diego Padres in the 8th round of the 2003 amateur draft. Player signed June 10, 2003.
July 22, 2003: Jesse Orosco was sent to the New York Yankees by the San Diego Padres as part of a conditional deal.
August 26, 2003: Jason Bay was traded by the San Diego Padres with a player to be named later and Oliver Perez to the Pittsburgh Pirates for Brian Giles. The San Diego Padres sent Corey Stewart (minors) (October 2, 2003) to the Pittsburgh Pirates to complete the trade.
August 29, 2003: Jaret Wright was selected off waivers by the Atlanta Braves from the San Diego Padres.