List of San Diego Padres minor league affiliates

The San Diego Padres farm system consists of seven Minor League Baseball affiliates across the United States and in the Dominican Republic. Four affiliates are independently owned, while three—the Arizona Complex League Padres and two Dominican Summer League Padres squads—are owned by the major league club.

The Padres have been affiliated with the High-A Fort Wayne TinCaps of the Midwest League since 1999, making it the longest-running affiliation in the organization among teams not owned by the Padres. Their newest affiliate is the San Antonio Missions of the Texas League, which became the Padres' Double-A club in 2021.

Geographically, San Diego's closest domestic affiliate is the Single-A Lake Elsinore Storm of the California League, which is approximately 66 mi away. San Diego's furthest domestic affiliate is the Fort Wayne TinCaps some 1849 mi away.

Current affiliates
The San Diego Padres farm system consists of seven minor league affiliates.

1969–1989
Prior to the 1963 season, Major League Baseball (MLB) initiated a reorganization of Minor League Baseball that resulted in a reduction from six classes to four (Triple-A, Double-A, Class A, and Rookie) in response to the general decline of the minors throughout the 1950s and early-1960s when leagues and teams folded due to shrinking attendance caused by baseball fans' preference for staying at home to watch MLB games on television. The only change made within the next 27 years was Class A being subdivided for the first time to form Class A Short Season in 1966.

1990–2020
Minor League Baseball operated with six classes from 1990 to 2020. In 1990, the Class A level was subdivided for a second time with the creation of Class A-Advanced. The Rookie level consisted of domestic and foreign circuits.

2021–present
The current structure of Minor League Baseball is the result of an overall contraction of the system beginning with the 2021 season. Class A was reduced to two levels: High-A and Low-A. Low-A was reclassified as Single-A in 2022.