- New York Mets selected Joe Christopher in free agent draft on October 10, 1961.
- New York Mets selected Al Jackson in free agent draft on October 10, 1961.
- New York Mets traded Jim Marshall to the Pittsburgh Pirates for Vinegar Bend Mizell on May 6, 1962.
- New York Mets purchased Larry Foss from the Pittsburgh Pirates on September 6, 1962.
- New York Mets selected Jerry Hinsley in free agent draft on December 2, 1963.
- New York Mets traded Dennis Ribant and Gary Kolb to the Pittsburgh Pirates for Don Cardwell and Don Bosch on December 6, 1966.
- New York Mets sold Al Luplow to the Pittsburgh Pirates on June 21, 1967.
- New York Mets traded Duffy Dyer to the Pittsburgh Pirates for Gene Clines on October 22, 1974.
- New York Mets traded Tim Foli and Greg Field to the Pittsburgh Pirates for Frank Taveras on April 19, 1979.
- New York Mets sold Dock Ellis to the Pittsburgh Pirates on September 21, 1979.
- Pittsburgh Pirates signed Andy Hassler of the New York Mets as a free agent on November 21, 1979.
- New York Mets traded Marvell Wynne and Steve Senteney to the Pittsburgh Pirates for Junior Ortiz and Art Ray on June 14, 1983.
- New York Mets selected Junior Ortiz in free agent draft on December 3, 1984.
- New York Mets traded Al Pedrique and Scott Little to the Pittsburgh Pirates for Bill Almon on May 29, 1987.
- New York Mets traded Randy Milligan and Scott Henion to the Pittsburgh Pirates for Mackey Sasser and Tim Drummond on March 26, 1988.
- Pittsburgh Pirates claimed Terry McDaniel of the New York Mets on waivers on November 19, 1991.
- New York Mets signed free agent Bobby Bonilla of the Pittsburgh Pirates on December 2, 1991.
- Pittsburgh Pirates claimed Mark Dewey of the New York Mets on waivers on May 11, 1993.
- New York Mets claimed Blas Minor on waivers from the Pittsburgh Pirates on November 4, 1994.
- Pittsburgh Pirates signed Mike Maddux of the New York Mets as a free agent on April 10, 1995.
- Pittsburgh Pirates signed Steve Bieser of the New York Mets as a free agent on December 18, 1997.
- Pittsburgh Pirates signed Derek Bell of the New York Mets as a free agent on December 10, 2000.
- New York Mets purchased Gary Matthews from the Pittsburgh Pirates on December 28, 2001.
- Pittsburgh Pirates signed Jeff D'Amico of the New York Mets as a free agent on January 17, 2003.
- New York Mets sold Jorge Toca to the Pittsburgh Pirates on August 22, 2003.
- New York Mets traded Ty Wigginton, Jose Bautista and Matt Peterson to the Pittsburgh Pirates for Kris Benson and Jeff Keppinger on July 30, 2004.
- New York Mets selected Henry Owens in free agent draft on December 13, 2004.
- Pittsburgh Pirates signed Roberto Hernandez of the New York Mets as a free agent on December 15, 2005.
- New York Mets traded Xavier Nady to the Pittsburgh Pirates for Oliver Perez and Roberto Hernandez on July 31, 2006.
- New York Mets signed free agent Tony Armas of the Pittsburgh Pirates on February 11, 2008.
- Pittsburgh Pirates signed Fernando Nieve of the New York Mets as a free agent on December 2, 2010.
- Pittsburgh Pirates signed Nick Evans of the New York Mets as a free agent on November 30, 2011.
- New York Mets signed free agent Garrett Olson of the Pittsburgh Pirates on December 9, 2011.
- New York Mets claimed Jeremy Hefner on waivers from the Pittsburgh Pirates on December 12, 2011.
- New York Mets signed free agent Ronny Cedeno of the Pittsburgh Pirates on January 13, 2012.
- New York Mets traded Marlon Byrd and John Buck to the Pittsburgh Pirates for Vic Black and Dilson Herrera on August 27, 2013.
- New York Mets traded Ike Davis to the Pittsburgh Pirates for Zack Thornton and Blake Taylor on April 18, 2014.
- New York Mets traded Jon Niese to the Pittsburgh Pirates for Neil Walker on December 9, 2015.
- New York Mets signed free agent Antonio Bastardo of the Pittsburgh Pirates on January 22, 2016.
- Pittsburgh Pirates signed Eric O'Flaherty of the New York Mets as a free agent on February 11, 2016.
- New York Mets traded Antonio Bastardo to the Pittsburgh Pirates for Jon Niese on August 1, 2016.
- New York Mets traded Josh Smoker to the Pittsburgh Pirates for Daniel Zamora on January 31, 2018.
- New York Mets sold Tyler Bashlor to the Pittsburgh Pirates on August 2, 2020.
- New York Mets claimed Guillermo Heredia on waivers from the Pittsburgh Pirates on August 28, 2020.
- Pittsburgh Pirates signed Chasen Shreve of the New York Mets as a free agent on February 7, 2021.
- Pittsburgh Pirates signed Todd Frazier of the New York Mets as a free agent on February 20, 2021.
- New York Mets claimed Geoff Hartlieb on waivers from the Pittsburgh Pirates on July 9, 2021.
- Pittsburgh Pirates claimed Anthony Banda of the New York Mets on waivers on August 2, 2021.
- Pittsburgh Pirates signed Jerad Eickhoff of the New York Mets as a free agent on November 28, 2021.
- Pittsburgh Pirates signed Heath Hembree of the New York Mets as a free agent on March 15, 2022.
- New York Mets purchased Adonis Medina from the Pittsburgh Pirates on April 7, 2022.
- New York Mets traded Colin Holderman to the Pittsburgh Pirates for Daniel Vogelbach on July 22, 2022.
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