- New York Mets selected Jerry Morales in free agent draft on October 14, 1968.
- New York Mets selected Dick Selma in free agent draft on October 14, 1968.
- New York Mets traded Rod Gaspar to the San Diego Padres for Ron Herbel on September 1, 1970.
- New York Mets traded Dave Marshall to the San Diego Padres for Al Severinsen on November 30, 1972.
- New York Mets traded Jim McAndrew to the San Diego Padres for Steve Simpson on December 20, 1973.
- New York Mets traded Dave Kingman to the San Diego Padres for Bobby Valentine and Paul Siebert on June 15, 1977.
- New York Mets traded John Pacella and Jose Moreno to the San Diego Padres for Randy Jones on December 15, 1980.
- New York Mets traded Rusty Tillman to the San Diego Padres for Rick Lancellotti on March 31, 1985.
- New York Mets traded Kevin Mitchell, Stan Jefferson and Shawn Abner to the San Diego Padres for Kevin McReynolds, Gene Walter and Adam Ging on December 11, 1986.
- New York Mets traded Tim Teufel to the San Diego Padres for Garry Templeton on May 31, 1991.
- New York Mets traded Jeff Gardner to the San Diego Padres for Steve Rosenberg on December 11, 1991.
- New York Mets traded Terry Bross to the San Diego Padres for Craig Bullock on March 30, 1992.
- New York Mets traded Wally Whitehurst, D.J. Dozier and Raul Casanova to the San Diego Padres for Tony Fernandez on October 26, 1992.
- New York Mets traded Roger Mason and Mike Freitas to the San Diego Padres for Mike Maddux on December 17, 1992.
- New York Mets traded Marc Kroon and Randy Curtis to the San Diego Padres for Frank Seminara, Tracy Sanders and Pablo Martinez on December 10, 1993.
- New York Mets selected Charlie Greene in free agent draft on December 13, 1993.
- San Diego Padres signed Eric Gunderson of the New York Mets as a free agent on December 24, 1993.
- New York Mets selected Jason Hardtke in free agent draft on December 5, 1994.
- New York Mets selected Shawn Hare in free agent draft on December 5, 1994.
- New York Mets traded Jeff Barry to the San Diego Padres for Pedro Martinez on December 15, 1995.
- New York Mets traded Pete Walker and Luis Arroyo to the San Diego Padres for Roberto Petagine and Scott Adair on March 17, 1996.
- San Diego Padres signed Chris Jones of the New York Mets as a free agent on November 4, 1996.
- New York Mets claimed Jason Middlebrook on waivers from the San Diego Padres on October 5, 2000.
- New York Mets claimed Desi Relaford on waivers from the San Diego Padres on October 12, 2000.
- San Diego Padres claimed Jason Middlebrook of the New York Mets on waivers on November 22, 2000.
- New York Mets traded Bubba Trammell to the San Diego Padres for Donne Wall on December 11, 2000.
- San Diego Padres signed Bobby Jones of the New York Mets as a free agent on February 15, 2001.
- New York Mets traded Bobby Jones, Jason Bay and Josh Reynolds to the San Diego Padres for Jason Middlebrook and Steve Reed on July 31, 2002.
- New York Mets traded Mike Cameron to the San Diego Padres for Xavier Nady on November 18, 2005.
- San Diego Padres signed Eric Valent of the New York Mets as a free agent on January 12, 2006.
- San Diego Padres signed Mike Piazza of the New York Mets as a free agent on January 31, 2006.
- New York Mets traded Heath Bell and Royce Ring to the San Diego Padres for Jon Adkins and Ben Johnson on November 15, 2006.
- San Diego Padres signed Chip Ambres of the New York Mets as a free agent on November 15, 2007.
- New York Mets signed free agent Henry Blanco of the San Diego Padres on December 4, 2009.
- New York Mets signed free agent Chris Young of the San Diego Padres on January 17, 2011.
- New York Mets signed free agent Scott Hairston of the San Diego Padres on January 20, 2011.
- New York Mets traded Eddie Kunz to the San Diego Padres for Allan Dykstra on March 29, 2011.
- New York Mets claimed Mike Baxter on waivers from the San Diego Padres on July 22, 2011.
- San Diego Padres signed Dale Thayer of the New York Mets as a free agent on December 6, 2011.
- New York Mets signed free agent Rob Johnson of the San Diego Padres on December 21, 2011.
- New York Mets traded Cory Mazzoni to the San Diego Padres for Alex Torres on March 30, 2015.
- New York Mets purchased James Loney from the San Diego Padres on May 28, 2016.
- New York Mets claimed Buddy Baumann on waivers from the San Diego Padres on April 27, 2018.
- San Diego Padres signed Seth Lugo of the New York Mets as a free agent on December 22, 2022.
- San Diego Padres claimed Gary Sanchez of the New York Mets on waivers on May 29, 2023.
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