- New York Mets traded Hobie Landrith to the Baltimore Orioles for Marv Throneberry on May 9, 1962.
- New York Mets purchased Bob Johnson and John Miller from the Baltimore Orioles on May 10, 1967.
- New York Mets signed free agent Elliott Maddox of the Baltimore Orioles on November 30, 1977.
- Baltimore Orioles signed Ray Knight of the New York Mets as a free agent on February 12, 1987.
- New York Mets traded Doug Sisk to the Baltimore Orioles for Blaine Beatty and Greg Talamantez on December 7, 1987.
- New York Mets traded John Mitchell and Joaquin Contreras to the Baltimore Orioles for Keith Hughes and Cesar Mejia on December 5, 1989.
- New York Mets signed free agent Jeff McKnight of the Baltimore Orioles on December 20, 1991.
- Baltimore Orioles signed Sid Fernandez of the New York Mets as a free agent on November 22, 1993.
- New York Mets traded Kevin Baez and Tom Wegmann to the Baltimore Orioles for David Segui on March 27, 1994.
- Baltimore Orioles signed Frank Seminara of the New York Mets as a free agent on November 23, 1994.
- New York Mets traded Bobby Bonilla and Jimmy Williams to the Baltimore Orioles for Alex Ochoa and Damon Buford on July 28, 1995.
- New York Mets traded Hector Ramirez to the Baltimore Orioles for Manny Alexander and Scott McClain on March 22, 1997.
- Baltimore Orioles claimed Charlie Greene of the New York Mets on waivers on September 11, 1997.
- Baltimore Orioles claimed Rich Becker of the New York Mets on waivers on June 16, 1998.
- New York Mets traded Charles Johnson to the Baltimore Orioles for Armando Benitez on December 1, 1998.
- New York Mets traded Chuck McElroy to the Baltimore Orioles for Jesse Orosco on December 10, 1999.
- New York Mets traded Melvin Mora, Mike Kinkade, Pat Gorman and Leslie Brea to the Baltimore Orioles for Mike Bordick on July 28, 2000.
- Baltimore Orioles signed Mike Bordick of the New York Mets as a free agent on December 20, 2000.
- New York Mets traded Gary Matthews to the Baltimore Orioles for John Bale on April 3, 2002.
- New York Mets traded Karim Garcia to the Baltimore Orioles for Mike DeJean on July 19, 2004.
- New York Mets traded Kris Benson to the Baltimore Orioles for John Maine and Jorge Julio on January 21, 2006.
- Baltimore Orioles signed Tyler Yates of the New York Mets as a free agent on January 24, 2006.
- Baltimore Orioles signed Chad Bradford of the New York Mets as a free agent on November 30, 2006.
- New York Mets signed free agent David Newhan of the Baltimore Orioles on January 5, 2007.
- Baltimore Orioles signed Steve Trachsel of the New York Mets as a free agent on February 14, 2007.
- New York Mets signed free agent Gustavo Molina of the Baltimore Orioles on December 4, 2007.
- New York Mets signed free agent Omir Santos of the Baltimore Orioles on December 23, 2008.
- New York Mets claimed Justin Turner on waivers from the Baltimore Orioles on May 25, 2010.
- New York Mets selected Pedro Beato in free agent draft on December 9, 2010.
- Baltimore Orioles signed Ronny Paulino of the New York Mets as a free agent on January 31, 2012.
- New York Mets sold Omar Quintanilla to the Baltimore Orioles on July 20, 2012.
- New York Mets signed free agent Omar Quintanilla of the Baltimore Orioles on January 4, 2013.
- New York Mets signed free agent Taylor Teagarden of the Baltimore Orioles on January 6, 2014.
- Baltimore Orioles signed Johan Santana of the New York Mets as a free agent on March 14, 2014.
- New York Mets selected Logan Verrett in free agent draft on December 11, 2014.
- New York Mets sold Logan Verrett to the Baltimore Orioles on November 30, 2016.
- New York Mets sold Gabriel Ynoa to the Baltimore Orioles on February 10, 2017.
- Baltimore Orioles signed Josh Edgin of the New York Mets as a free agent on November 28, 2017.
- New York Mets signed free agent Ryan O'Rourke of the Baltimore Orioles on November 15, 2018.
- New York Mets signed free agent Ruben Tejada of the Baltimore Orioles on March 23, 2019.
- New York Mets sold Keon Broxton to the Baltimore Orioles on May 22, 2019.
- Baltimore Orioles claimed Eric Hanhold of the New York Mets on waivers on September 16, 2019.
- New York Mets traded Kevin Smith to the Baltimore Orioles for Miguel Castro on August 31, 2020.
- New York Mets claimed Chance Sisco on waivers from the Baltimore Orioles on June 25, 2021.
- Baltimore Orioles signed Mychal Givens of the New York Mets as a free agent on December 21, 2022.
- New York Mets signed free agent DJ Stewart of the Baltimore Orioles on February 2, 2023.
- New York Mets claimed Reed Garrett on waivers from the Baltimore Orioles on June 25, 2023.
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