- New York Mets selected Steve Dillon in free agent draft on November 26, 1962.
- New York Mets selected Duke Carmel in free agent draft on November 30, 1964.
- New York Mets purchased Bob Friend from the New York Yankees on June 15, 1966.
- New York Mets sold Chris Cannizzaro to the New York Yankees on December 7, 1966.
- New York Mets purchased Hal Reniff from the New York Yankees on June 29, 1967.
- New York Mets traded Roy Staiger to the New York Yankees for Sergio Ferrer on December 9, 1977.
- New York Mets purchased Ray Burris from the New York Yankees on August 20, 1979.
- New York Mets traded Felix Perdomo and Steve Ray to the New York Yankees for Tucker Ashford on April 18, 1983.
- New York Mets traded Rafael Santana and Victor Garcia to the New York Yankees for Phil Lombardi, Darren Reed and Steve Frey on December 11, 1987.
- New York Yankees signed John Candelaria of the New York Mets as a free agent on January 15, 1988.
- New York Mets traded Tim Burke to the New York Yankees for Lee Guetterman on June 9, 1992.
- New York Mets selected Mike Draper in free agent draft on December 7, 1992.
- New York Mets traded Frank Tanana to the New York Yankees for Kenny Greer on September 17, 1993.
- New York Yankees signed Dwight Gooden of the New York Mets as a free agent on February 20, 1996.
- New York Yankees claimed Darren Bragg of the New York Mets on waivers on June 12, 2001.
- New York Mets traded Robin Ventura to the New York Yankees for David Justice on December 7, 2001.
- New York Mets signed free agent Mike Stanton of the New York Yankees on December 16, 2002.
- New York Mets traded Armando Benitez to the New York Yankees for Jason Anderson, Anderson Garcia and Ryan Bicondoa on July 16, 2003.
- New York Yankees signed Tony Clark of the New York Mets as a free agent on January 12, 2004.
- New York Mets signed free agent Karim Garcia of the New York Yankees on January 20, 2004.
- New York Mets traded Mike Stanton to the New York Yankees for Felix Heredia on December 3, 2004.
- New York Mets signed free agent Miguel Cairo of the New York Yankees on January 10, 2005.
- New York Mets signed free agent Fernando Martinez of the New York Yankees on July 2, 2005.
- New York Yankees signed Miguel Cairo of the New York Mets as a free agent on January 5, 2006.
- New York Yankees signed Casey Fossum of the New York Mets as a free agent on May 1, 2009.
- New York Yankees signed Rene Rivera of the New York Mets as a free agent on May 21, 2010.
- New York Yankees signed Pedro Feliciano of the New York Mets as a free agent on January 3, 2011.
- New York Yankees signed Mike O'Connor of the New York Mets as a free agent on November 16, 2011.
- New York Mets claimed Chris Schwinden on waivers from the New York Yankees on July 5, 2012.
- New York Mets signed free agent Pedro Feliciano of the New York Yankees on January 21, 2013.
- New York Mets signed free agent Curtis Granderson of the New York Yankees on December 9, 2013.
- New York Mets sold Gonzalez Germen to the New York Yankees on December 19, 2014.
- New York Mets signed free agent Todd Frazier of the New York Yankees on February 7, 2018.
- New York Mets signed free agent Adeiny Hechavarria of the New York Yankees on February 18, 2019.
- New York Mets signed free agent Dellin Betances of the New York Yankees on December 24, 2019.
- New York Yankees signed Luis Avilan of the New York Mets as a free agent on February 3, 2020.
- New York Yankees signed Robinson Chirinos of the New York Mets as a free agent on February 13, 2021.
- New York Yankees signed Jose Peraza of the New York Mets as a free agent on November 28, 2021.
- New York Mets traded Miguel Castro to the New York Yankees for Joely Rodriguez on April 3, 2022.
- New York Yankees claimed Michael Tonkin of the New York Mets on waivers on April 25, 2024.
- New York Mets purchased Luis Torrens from the New York Yankees on May 31, 2024.
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