- 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 traded Jerson Perez to the Toronto Blue Jays for Jim Mann on March 22, 2000.
- 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 sold Brad Emaus to the Toronto Blue Jays on April 21, 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.
- Toronto Blue Jays claimed Chris Schwinden of the New York Mets on waivers on June 2, 2012.
- New York Mets traded R.A. Dickey, Josh Thole and Mike Nickeas to the Toronto Blue Jays for Travis d'Arnaud, Noah Syndergaard, John Buck and Wuilmer Becerra on December 17, 2012.
- New York Mets signed free agent Aaron Laffey of the Toronto Blue Jays on December 27, 2012.
- New York Mets signed free agent Brandon Lyon of the Toronto Blue Jays on February 8, 2013.
- Toronto Blue Jays claimed Aaron Laffey of the New York Mets on waivers on April 13, 2013.
- New York Mets signed free agent John Mayberry of the Toronto Blue Jays on December 15, 2014.
- New York Mets sold Darrell Ceciliani to the Toronto Blue Jays on February 2, 2016.
- Toronto Blue Jays claimed Ty Kelly of the New York Mets on waivers on April 10, 2017.
- New York Mets sold Wilmer Font to the Toronto Blue Jays on July 19, 2019.
- New York Mets traded Anthony Kay and Simeon Woods-Richardson to the Toronto Blue Jays for Marcus Stroman on July 28, 2019.
- Toronto Blue Jays signed Ruben Tejada of the New York Mets as a free agent on January 20, 2020.
- Toronto Blue Jays signed Joe Panik of the New York Mets as a free agent on January 20, 2020.
- New York Mets signed free agent Brandon Drury of the Toronto Blue Jays on January 5, 2021.
- New York Mets traded Steven Matz to the Toronto Blue Jays for Yennsy Diaz, Sean Reid-Foley and Josh Winckowski on January 27, 2021.
- New York Mets signed free agent Jonathan Villar of the Toronto Blue Jays on February 11, 2021.
- New York Mets signed free agent Taijuan Walker of the Toronto Blue Jays on February 20, 2021.
- New York Mets claimed Brad Hand on waivers from the Toronto Blue Jays on September 2, 2021.
- Toronto Blue Jays signed Chris Bassitt of the New York Mets as a free agent on December 16, 2022.
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