- 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, Ryan Bicondoa and Anderson Garcia 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 Pedro Feliciano of the New York Mets as a free agent on January 3, 2011.
- New York Mets signed free agent Pedro Feliciano of the New York Yankees on January 21, 2013.
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