| 1980 | Harbison: Piano Concerto / Stock: Inner Space | John Harbison, David Stock; American Composers Orchestra, Gunther Schuller, Robert Miller | | 1 |
| 1986 | Ulysses Bow / Samuel Chapter | John Harbison | | 2 |
| 1993 | American Contemporaries | John Harbison, Richard Wernick, Gunther Schuller; Emerson String Quartet | | 2 |
| 1994 | Harbison: Oboe Concerto / Symphony no. 2 / Sessions: Symphony no. 2 | John Harbison, Roger Sessions; San Francisco Symphony, Herbert Blomstedt, William Bennett | | 1 |
| 1995 | Voices Within | Druckman, Harbison, Schwantner, Zwilich; Ensemble 21, Arthur Weisberg | | 1 |
| 1996 | The Boston Collection | John Harbison; Karol Bennett, Judith Gordon, Rose Mary Harbison, Randall Hodgkinson, Robert Levin, John McDonald, Fenwick Smith | | 1 |
| 1997 | World Premiere Recordings: Violin Concerto / Recordare / Seven Motets | John Harbison; Rose Mary Harbison, Emmanuel Music, Craig Smith | | 1 |
| 1998 | Lukasik: Concertino / Theofanidis: Netherland / Harbison: San Antonio / Tisinai: Trio / Gillingham: Alto Saxophone Sonata | Lukasik, Theofanidis, Harbison, Tisinai, Gillingham; Tom Myer | | 1 |
| 1999 | Rands: Ceremonial / Harbison: Olympic Dances / Kraft / Concerto for Four Solo Percussion and Wind Ensemble / Husa: Les Couleurs fauves | Bernard Rands, John Harbison, William Kraft, Karel Husa; New England Conservatory Wind Ensemble, Frank L. Battisti | | 1 |
| 2006 | Music of John Harbison, Volume 1 | John Harbison | | 1 |
| 2006 | Songs America Loves to Sing: Old & New Music for Winds, Strings & Piano | Harbison, Mozart, Dello Joio, Bunch; Atlanta Chamber Players | | 1 |
| 2014 | String Trio / Four Songs of Solitude / Songs America Loves to Sing | John Harbison; Members of Camerata Pacifica | | 1 |
| 2015 | Songs After Hours | John Harbison; Mary Mackenzie, John Chin | | 1 |
| 2018 | Double Concertos | Brahms, Rihm, Harbison; Jan Vogler, Mira Wang, Royal Scottish National Orchestra, Peter Oundjian | | 1 |
| 2018 | John Harbison: Symphony no. 4 / Carl Ruggles: Sun-Treader / Steven Stucky: Second Concerto for Orchestra | John Harbison, Carl Ruggles, Steven Stucky; National Orchestral Institute Philharmonic, David Alan Miller | | 2 |
| 2018 | Beethoven / Mozart / Harbison | Beethoven, Mozart, Harbison; David Deveau, Borromeo String Quartet, Jessica Bodner, Thomas van Dyck | | 2 |
| 2018 | Requiem | John Harbison; Jessica Rivera, Michaela Martens, Nicholas Phan, Kelly Markgraf, Nashville Symphony Orchestra, Nashville Symphony Chorus, Giancarlo Guerrero | | 1 |
| 2020 | Bach & Beyond, Part 3 | Bach, Harbison, Berio; Jennifer Koh | | 3 |
| 2020 | Gershwin: Concerto in F / Tower: Sequoia / Piston: Symphony no. 5 / Harbison: Remembering Gatsby | Gershwin, Tower, Piston, Harbison; Kevin Cole, National Orchestral Institute Philharmonic, David Alan Miller | | 1 |
| — | Spectrum: New American Music Volume III | Jacob Druckman, Joseph Schwantner, John Harbison | | 1 |
