- New York Mets traded Jerry Koosman to the Minnesota Twins for Jesse Orosco and Greg Field on December 8, 1978.
- New York Mets signed free agent Mike Cubbage of the Minnesota Twins on December 19, 1980.
- New York Mets traded Billy Beane, Bill Latham and Joe Klink to the Minnesota Twins for Tim Teufel and Pat Crosby on January 16, 1986.
- New York Mets traded Ron Gardenhire to the Minnesota Twins for Donnie Iasparro on November 12, 1986.
- Minnesota Twins signed Randy Niemann of the New York Mets as a free agent on January 16, 1987.
- New York Mets traded Jason Felice to the Minnesota Twins for Bill Latham on May 10, 1987.
- Minnesota Twins signed Don Schulze of the New York Mets as a free agent on December 7, 1987.
- New York Mets traded Wally Backman and Mike Santiago to the Minnesota Twins for Toby Nivens, Steve Gasser and Jeff Bumgarner on December 7, 1988.
- New York Mets traded Rick Aguilera, David West, Kevin Tapani, Tim Drummond and Jack Savage to the Minnesota Twins for Frank Viola on July 31, 1989.
- New York Mets signed free agent Orlando Mercado of the Minnesota Twins on December 12, 1989.
- New York Mets signed free agent Kelvin Torve of the Minnesota Twins on December 13, 1989.
- New York Mets selected Doug Simons in free agent draft on December 3, 1990.
- New York Mets traded Pat Howell to the Minnesota Twins for Darren Reed on November 18, 1992.
- Minnesota Twins signed Jeff Innis of the New York Mets as a free agent on February 3, 1994.
- New York Mets traded Alex Ochoa to the Minnesota Twins for Rich Becker on December 12, 1997.
- New York Mets traded Rick Reed to the Minnesota Twins for Matt Lawton on July 30, 2001.
- Minnesota Twins signed Pat Strange of the New York Mets as a free agent on December 21, 2004.
- New York Mets traded Drew Butera and Dustin Martin to the Minnesota Twins for Luis Castillo on July 30, 2007.
- New York Mets traded Carlos Gomez, Philip Humber, Deolis Guerra and Kevin Mulvey to the Minnesota Twins for Johan Santana on February 2, 2008.
- Minnesota Twins signed Luis Ayala of the New York Mets as a free agent on February 18, 2009.
- New York Mets signed free agent R.A. Dickey of the Minnesota Twins on December 21, 2009.
- New York Mets claimed Jason Pridie on waivers from the Minnesota Twins on February 9, 2010.
- Minnesota Twins signed Mike Pelfrey of the New York Mets as a free agent on December 17, 2012.
- New York Mets selected Sean Gilmartin in free agent draft on December 11, 2014.
- Minnesota Twins signed Wilfredo Tovar of the New York Mets as a free agent on December 14, 2015.
- Minnesota Twins claimed Adam Wilk of the New York Mets on waivers on May 10, 2017.
- New York Mets signed free agent Trevor May of the Minnesota Twins on December 2, 2020.
- New York Mets sold Michael Tonkin to the Minnesota Twins on April 9, 2024.
- New York Mets claimed Michael Tonkin on waivers from the Minnesota Twins on April 17, 2024.
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