- New York Mets purchased Galen Cisco from the Boston Red Sox on September 7, 1962.
- New York Mets traded Felix Mantilla to the Boston Red Sox for Tracy Stallard, Pumpsie Green and Al Moran on December 11, 1962.
- New York Mets traded Joe Christopher to the Boston Red Sox for Eddie Bressoud on November 30, 1965.
- New York Mets sold Galen Cisco to the Boston Red Sox on June 6, 1966.
- New York Mets selected Amos Otis in free agent draft on November 28, 1966.
- New York Mets traded Al Yates to the Boston Red Sox for Dennis Bennett on June 24, 1967.
- New York Mets sold Cal Koonce to the Boston Red Sox on June 8, 1970.
- New York Mets traded Leo Foster to the Boston Red Sox for Jim Burton on March 29, 1978.
- New York Mets purchased Andy Hassler from the Boston Red Sox on June 15, 1979.
- Boston Red Sox signed Skip Lockwood of the New York Mets as a free agent on November 27, 1979.
- New York Mets traded Mike Davis to the Boston Red Sox for Mike Torrez on January 13, 1983.
- New York Mets sold Ed Glynn to the Boston Red Sox on November 9, 1984.
- New York Mets traded Calvin Schiraldi, John Christensen, Wes Gardner and La Schelle Tarver to the Boston Red Sox for Bob Ojeda, John Mitchell, Chris Bayer and Tom McCarthy on November 13, 1985.
- New York Mets traded Mike Marshall to the Boston Red Sox for Greg Hansell, Paul Williams and Ed Perozo on July 27, 1990.
- Boston Red Sox signed Frank Viola of the New York Mets as a free agent on January 2, 1992.
- New York Mets signed free agent Don Florence of the Boston Red Sox on November 16, 1994.
- New York Mets selected Joe Crawford in free agent draft on December 4, 1995.
- New York Mets purchased Joe Crawford from the Boston Red Sox on March 26, 1996.
- New York Mets traded Toby Borland to the Boston Red Sox for Ricky Trlicek on May 12, 1997.
- Boston Red Sox signed Brad Clontz of the New York Mets as a free agent on December 14, 1998.
- New York Mets traded Jermaine Allensworth to the Boston Red Sox for Jon Nunnally on November 12, 1999.
- New York Mets signed free agent Cliff Floyd of the Boston Red Sox on December 20, 2002.
- New York Mets signed free agent Rey Sanchez of the Boston Red Sox on December 27, 2002.
- Boston Red Sox claimed Edwin Almonte of the New York Mets on waivers on November 20, 2003.
- New York Mets signed free agent Pedro Martinez of the Boston Red Sox on December 16, 2004.
- New York Mets traded Ian Bladergroen to the Boston Red Sox for Doug Mientkiewicz on January 26, 2005.
- New York Mets signed free agent Chad Bradford of the Boston Red Sox on December 21, 2005.
- New York Mets signed free agent Geremi Gonzalez of the Boston Red Sox on January 24, 2006.
- New York Mets signed free agent Chip Ambres of the Boston Red Sox on December 19, 2006.
- New York Mets signed free agent Alex Cora of the Boston Red Sox on January 22, 2009.
- New York Mets signed free agent Jon Switzer of the Boston Red Sox on January 26, 2009.
- New York Mets traded Billy Wagner to the Boston Red Sox for Chris Carter and Eddie Lora on August 25, 2009.
- New York Mets signed free agent Jason Bay of the Boston Red Sox on January 5, 2010.
- New York Mets traded Pedro Beato to the Boston Red Sox for Kelly Shoppach on August 14, 2012.
- New York Mets signed free agent Scott Atchison of the Boston Red Sox on January 29, 2013.
- Boston Red Sox signed Dana Eveland of the New York Mets as a free agent on January 21, 2015.
- New York Mets traded Addison Reed to the Boston Red Sox for Jamie Callahan, Gerson Bautista and Stephen Nogosek on July 31, 2017.
- New York Mets signed free agent Rick Porcello of the Boston Red Sox on December 16, 2019.
- Boston Red Sox claimed Chris Mazza of the New York Mets on waivers on December 20, 2019.
- New York Mets signed free agent Erasmo Ramirez of the Boston Red Sox on January 24, 2020.
- New York Mets signed free agent Jose Peraza of the Boston Red Sox on November 4, 2020.
- Boston Red Sox claimed Geoff Hartlieb of the New York Mets on waivers on September 4, 2021.
- Boston Red Sox signed Rich Hill of the New York Mets as a free agent on December 1, 2021.
- New York Mets signed free agent Adam Ottavino of the Boston Red Sox on March 14, 2022.
- New York Mets claimed Yolmer Sanchez on waivers from the Boston Red Sox on August 18, 2022.
- Boston Red Sox signed Joely Rodriguez of the New York Mets as a free agent on November 23, 2022.
- New York Mets signed free agent Tommy Pham of the Boston Red Sox on January 24, 2023.
- New York Mets sold Zack Short to the Boston Red Sox on May 1, 2024.
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