- New York Mets selected Ray Daviault in free agent draft on October 10, 1961.
- New York Mets selected Hobie Landrith in free agent draft on October 10, 1961.
- New York Mets purchased Joe Pignatano from the San Francisco Giants on July 13, 1962.
- New York Mets selected Jack Fisher in free agent draft on October 10, 1963.
- New York Mets sold Duke Snider to the San Francisco Giants on April 14, 1964.
- New York Mets purchased Chuck Hiller from the San Francisco Giants on May 11, 1965.
- New York Mets purchased Bob Shaw from the San Francisco Giants on June 10, 1966.
- New York Mets traded Jim Gosger and Bob Heise to the San Francisco Giants for Ray Sadecki and Dave Marshall on December 12, 1969.
- New York Mets traded Charlie Williams to the San Francisco Giants for Willie Mays on May 11, 1972.
- New York Mets purchased Dave Kingman from the San Francisco Giants on February 28, 1975.
- New York Mets purchased Mike Phillips from the San Francisco Giants on May 3, 1975.
- New York Mets traded Bob Gallagher to the San Francisco Giants for Leon Brown on March 16, 1976.
- New York Mets purchased Tim Foli from the San Francisco Giants on December 7, 1977.
- New York Mets claimed Mark Dewey on waivers from the San Francisco Giants on May 9, 1991.
- New York Mets traded Rob Katzaroff to the San Francisco Giants for Kevin Bass on August 8, 1992.
- San Francisco Giants signed Kenny Greer of the New York Mets as a free agent on November 29, 1994.
- San Francisco Giants signed Kevin Roberson of the New York Mets as a free agent on November 25, 1996.
- New York Mets traded Tsuyoshi Shinjo and Desi Relaford to the San Francisco Giants for Shawn Estes on December 16, 2001.
- San Francisco Giants signed Edgardo Alfonzo of the New York Mets as a free agent on December 15, 2002.
- New York Mets signed free agent Tsuyoshi Shinjo of the San Francisco Giants on January 11, 2003.
- New York Mets signed free agent Moises Alou of the San Francisco Giants on November 20, 2006.
- New York Mets claimed Pat Misch on waivers from the San Francisco Giants on June 5, 2009.
- San Francisco Giants signed Elmer Dessens of the New York Mets as a free agent on February 8, 2011.
- New York Mets traded Carlos Beltran to the San Francisco Giants for Zack Wheeler on July 28, 2011.
- New York Mets traded Angel Pagan to the San Francisco Giants for Andres Torres and Ramon Ramirez on December 6, 2011.
- San Francisco Giants signed Andres Torres of the New York Mets as a free agent on December 13, 2012.
- San Francisco Giants signed Ramon Ramirez of the New York Mets as a free agent on February 4, 2013.
- New York Mets signed free agent Alejandro De Aza of the San Francisco Giants on December 23, 2015.
- San Francisco Giants signed Justin Ruggiano of the New York Mets as a free agent on December 16, 2016.
- San Francisco Giants signed Jamie Callahan of the New York Mets as a free agent on January 24, 2019.
- New York Mets claimed Aaron Altherr on waivers from the San Francisco Giants on May 23, 2019.
- New York Mets traded Jordan Humphreys to the San Francisco Giants for Billy Hamilton on August 2, 2020.
- San Francisco Giants claimed Trevor Hildenberger of the New York Mets on waivers on May 18, 2021.
- New York Mets claimed Nick Tropeano on waivers from the San Francisco Giants on June 11, 2021.
- New York Mets traded Will Toffey to the San Francisco Giants for Anthony Banda on July 2, 2021.
- New York Mets traded J.D. Davis, Thomas Szapucki, Carson Seymour and Nick Zwack to the San Francisco Giants for Darin Ruf on August 2, 2022.
- New York Mets signed free agent Sean Manaea of the San Francisco Giants on January 12, 2024.
- New York Mets claimed Alex Young on waivers from the San Francisco Giants on July 17, 2024.
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