- New York Mets selected Bobby Smith in free agent draft on October 10, 1961.
- New York Mets selected Choo Choo Coleman in free agent draft on October 10, 1961.
- New York Mets traded Frank Thomas to the Philadelphia Phillies for Gary Kroll and Wayne Graham on August 7, 1964.
- New York Mets traded Bobby Klaus, Wayne Graham and Jimmie Schaffer to the Philadelphia Phillies for Dick Stuart on February 22, 1966.
- New York Mets purchased Dallas Green from the Philadelphia Phillies on July 22, 1966.
- New York Mets traded Chuck Hiller to the Philadelphia Phillies for Phil Linz on July 11, 1967.
- New York Mets selected Mike Bruhert in free agent draft on April 10, 1973.
- New York Mets traded Tug McGraw, Don Hahn and Dave Schneck to the Philadelphia Phillies for John Stearns, Del Unser and Mac Scarce on December 3, 1974.
- New York Mets traded Bud Harrelson to the Philadelphia Phillies for Fred Andrews on March 24, 1978.
- New York Mets traded Jackson Todd to the Philadelphia Phillies for Edward Cuervo on March 27, 1978.
- New York Mets sold Butch Metzger to the Philadelphia Phillies on July 4, 1978.
- New York Mets traded Nino Espinosa to the Philadelphia Phillies for Richie Hebner and Jose Moreno on March 27, 1979.
- New York Mets purchased Jose Cardenal from the Philadelphia Phillies on August 2, 1979.
- New York Mets traded Ronn Reynolds and Jeff Bittiger to the Philadelphia Phillies for Ronnie Gideon and Rodger Cole on January 16, 1986.
- New York Mets traded Bill Almon to the Philadelphia Phillies for Shawn Barton and Vladimir Perez on March 21, 1988.
- New York Mets traded Lenny Dykstra, Roger McDowell and Tom Edens to the Philadelphia Phillies for Juan Samuel on June 18, 1989.
- New York Mets traded Nikco Riesgo and Rocky Elli to the Philadelphia Phillies for Tom Herr on August 30, 1990.
- New York Mets traded Rico Brogna to the Philadelphia Phillies for Ricardo Jordan and Toby Borland on November 27, 1996.
- Philadelphia Phillies signed Yorkis Perez of the New York Mets as a free agent on January 23, 1998.
- Philadelphia Phillies signed Alberto Castillo of the New York Mets as a free agent on November 5, 1998.
- New York Mets traded Todd Pratt to the Philadelphia Phillies for Gary Bennett on July 23, 2001.
- New York Mets traded Turk Wendell and Dennis Cook to the Philadelphia Phillies for Bruce Chen and Adam Walker on July 27, 2001.
- New York Mets signed free agent Billy Wagner of the Philadelphia Phillies on November 29, 2005.
- New York Mets signed free agent Endy Chavez of the Philadelphia Phillies on December 22, 2005.
- Philadelphia Phillies signed Wilson Valdez of the New York Mets as a free agent on November 10, 2009.
- Philadelphia Phillies signed Brian Schneider of the New York Mets as a free agent on December 1, 2009.
- Philadelphia Phillies claimed Nelson Figueroa of the New York Mets on waivers on April 7, 2010.
- Philadelphia Phillies signed Pat Misch of the New York Mets as a free agent on November 29, 2011.
- New York Mets signed free agent John Lannan of the Philadelphia Phillies on January 18, 2014.
- New York Mets traded Asdrubal Cabrera to the Philadelphia Phillies for Franklyn Kilome on July 27, 2018.
- New York Mets signed free agent Wilson Ramos of the Philadelphia Phillies on December 18, 2018.
- New York Mets signed free agent Luis Avilan of the Philadelphia Phillies on January 10, 2019.
- New York Mets traded Jason Vargas to the Philadelphia Phillies for Austin Bossart on July 29, 2019.
- Philadelphia Phillies signed Zack Wheeler of the New York Mets as a free agent on December 9, 2019.
- Philadelphia Phillies signed Ryan Cordell of the New York Mets as a free agent on April 26, 2021.
- Philadelphia Phillies signed Brad Hand of the New York Mets as a free agent on March 15, 2022.
- New York Mets signed free agent Travis Jankowski of the Philadelphia Phillies on March 17, 2022.
- New York Mets claimed Sam Clay on waivers from the Philadelphia Phillies on July 10, 2022.
- New York Mets signed free agent David Robertson of the Philadelphia Phillies on December 9, 2022.
- Philadelphia Phillies signed Taijuan Walker of the New York Mets as a free agent on December 16, 2022.
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