- New York Mets selected Wayne Garrett in free agent draft on December 2, 1968.
- New York Mets sold Don Cardwell to the Atlanta Braves on July 12, 1970.
- New York Mets traded Ron Herbel to the Atlanta Braves for Bob Aspromonte on December 1, 1970.
- New York Mets traded Danny Frisella and Gary Gentry to the Atlanta Braves for Felix Millan and George Stone on November 1, 1972.
- New York Mets sold Buzz Capra to the Atlanta Braves on March 26, 1974.
- New York Mets purchased Jack Aker from the Atlanta Braves on June 14, 1974.
- New York Mets traded Joe Nolan to the Atlanta Braves for Leo Foster on April 4, 1975.
- Atlanta Braves signed Claudell Washington of the New York Mets as a free agent on November 15, 1980.
- New York Mets traded Tom Hausman to the Atlanta Braves for Carlos Diaz on September 10, 1982.
- Atlanta Braves signed Pete Falcone of the New York Mets as a free agent on January 27, 1983.
- New York Mets sold Mike Jorgensen to the Atlanta Braves on June 15, 1983.
- New York Mets traded Terry Blocker to the Atlanta Braves for Kevin Brown on November 11, 1987.
- Atlanta Braves claimed Phil Lombardi of the New York Mets on waivers on April 4, 1990.
- New York Mets traded Doug Sisk to the Atlanta Braves for Tony Valle on July 22, 1990.
- New York Mets traded Alejandro Pena to the Atlanta Braves for Tony Castillo and Joe Roa on August 28, 1991.
- Atlanta Braves signed Bill Pecota of the New York Mets as a free agent on January 4, 1993.
- New York Mets traded Dave Gallagher to the Atlanta Braves for Pete Smith on November 24, 1993.
- Atlanta Braves signed Charlie O'Brien of the New York Mets as a free agent on November 26, 1993.
- New York Mets selected Kevin Lomon in free agent draft on December 5, 1994.
- New York Mets sold Kevin Lomon to the Atlanta Braves on May 30, 1995.
- New York Mets traded Paul Byrd to the Atlanta Braves for Greg McMichael on November 25, 1996.
- New York Mets claimed Yorkis Perez on waivers from the Atlanta Braves on March 31, 1997.
- New York Mets signed free agent Tim Spehr of the Atlanta Braves on January 8, 1998.
- Atlanta Braves signed Kurt Abbott of the New York Mets as a free agent on December 13, 2000.
- New York Mets signed free agent Tom Glavine of the Atlanta Braves on December 5, 2002.
- Atlanta Braves signed Jorge Velandia of the New York Mets as a free agent on November 14, 2003.
- Atlanta Braves signed Joe DePastino of the New York Mets as a free agent on December 20, 2003.
- Atlanta Braves signed Esix Snead of the New York Mets as a free agent on November 10, 2004.
- New York Mets signed free agent Julio Franco of the Atlanta Braves on December 9, 2005.
- Atlanta Braves signed Chris Woodward of the New York Mets as a free agent on December 20, 2006.
- Atlanta Braves signed Tom Glavine of the New York Mets as a free agent on November 18, 2007.
- Atlanta Braves claimed Ruben Gotay of the New York Mets on waivers on March 28, 2008.
- New York Mets signed free agent Elmer Dessens of the Atlanta Braves on February 5, 2009.
- New York Mets traded Ryan Church to the Atlanta Braves for Jeff Francoeur on July 10, 2009.
- New York Mets claimed Manny Acosta on waivers from the Atlanta Braves on March 30, 2010.
- Atlanta Braves signed Eric Young of the New York Mets as a free agent on February 13, 2015.
- Atlanta Braves claimed Dario Alvarez of the New York Mets on waivers on May 25, 2015.
- New York Mets traded John Gant and Robert Whalen to the Atlanta Braves for Kelly Johnson and Juan Uribe on July 24, 2015.
- New York Mets purchased Eric Young from the Atlanta Braves on August 22, 2015.
- Atlanta Braves signed Alex Torres of the New York Mets as a free agent on January 7, 2016.
- Atlanta Braves signed Kelly Johnson of the New York Mets as a free agent on January 8, 2016.
- Atlanta Braves signed Carlos Torres of the New York Mets as a free agent on February 19, 2016.
- New York Mets traded Akeel Morris to the Atlanta Braves for Kelly Johnson on June 8, 2016.
- Atlanta Braves signed Bartolo Colon of the New York Mets as a free agent on November 17, 2016.
- Atlanta Braves claimed Guillermo Heredia of the New York Mets on waivers on February 24, 2021.
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