- New York Mets traded Roy Lee Jackson to the Toronto Blue Jays for Bob Bailor on December 12, 1980.
- New York Mets traded Mark Bomback to the Toronto Blue Jays for Charlie Puleo on April 6, 1981.
- New York Mets selected Lou Thornton in free agent draft on December 3, 1984.
- Toronto Blue Jays claimed Lee Mazzilli of the New York Mets on waivers on July 31, 1989.
- New York Mets traded Mookie Wilson to the Toronto Blue Jays for Jeff Musselman and Mike Brady on August 1, 1989.
- Toronto Blue Jays signed Pat Tabler of the New York Mets as a free agent on December 5, 1990.
- New York Mets traded David Cone to the Toronto Blue Jays for Jeff Kent and Ryan Thompson on August 27, 1992.
- Toronto Blue Jays signed Dick Schofield of the New York Mets as a free agent on January 15, 1993.
- New York Mets traded Tony Fernandez to the Toronto Blue Jays for Darrin Jackson on June 11, 1993.
- New York Mets traded Robert Person to the Toronto Blue Jays for John Olerud on December 20, 1996.
- New York Mets traded Leo Estrella to the Toronto Blue Jays for Tony Phillips on July 31, 1998.
- New York Mets signed free agent Steve Trachsel of the Toronto Blue Jays on December 11, 2000.
- Toronto Blue Jays claimed Pete Walker of the New York Mets on waivers on May 4, 2002.
- New York Mets signed free agent Chris Woodward of the Toronto Blue Jays on December 28, 2004.
- Toronto Blue Jays signed Victor Zambrano of the New York Mets as a free agent on January 30, 2007.
- Toronto Blue Jays signed Lance Broadway of the New York Mets as a free agent on December 16, 2009.
- Toronto Blue Jays signed Jeremy Reed of the New York Mets as a free agent on January 18, 2010.
- New York Mets signed free agent Rod Barajas of the Toronto Blue Jays on February 24, 2010.
- New York Mets sold Mike Jacobs to the Toronto Blue Jays on July 30, 2010.
- New York Mets selected Brad Emaus in free agent draft on December 9, 2010.
- New York Mets signed free agent Taylor Buchholz of the Toronto Blue Jays on January 3, 2011.
- New York Mets signed free agent Jon Rauch of the Toronto Blue Jays on December 14, 2011.
- New York Mets signed free agent Frank Francisco of the Toronto Blue Jays on December 19, 2011.
- New York Mets traded R. A. Dickey, Josh Thole and Mike Nickeas to the Toronto Blue Jays for John Buck, Travis d'Arnaud, Noah Syndergaard and Wuilmer Becerra on December 17, 2012.
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