Albums
- 1949: J. J. Johnson (Savoy)
- 1949: J. J. Johnson’s Jazz Quintets
- 1949: J. J. Johnson’s Boppers (Fantasy)
- 1949: J. J. Johnson with Sonny Stitt (OJC)
- 1952: Jazz South Pacific (Savoy)
- 1953: The Eminent Jay Jay Johnson Volume 1 Blue Note
- 1955: The Eminent Jay Jay Johnson Volume 2 Blue Note
- 1957: First Place American Jazz Classics
- 1957: Blue Trombone American Jazz Classics
- 1957: Stan Getz and J.J. Johnson at the Opera House
- 1960: J.J. Inc. Columbia
- 1963: J.J.’s Broadway (Verve)
- 1964: J.J.! (RCA)
- 1964: Proof Positive (Impulse!)
- 1965: Goodies (RCA)
- 1966: The Total (RCA)
- 1966: Broadway Express (RCA)
- 1977: The Yokohama Concert Pablo
- 1977: Chain Reaction: Yokohama Concert, Vol. 2 Pablo (released in 2002)
- 1979: Pinnacles OJC
- 1982: Aurex Jazz Festival ’82 All Star Jam Somethin’ Else Classics TOCJ
- 1983: Jackson, Johnson, Brown and Company Fantasy
- 1983: We’ll Be Together Again – J.J. Johnson and Joe Pass OJC
- 1984: Things Are Getting Better All the Time (w/ Al Grey) OJC
- 1988: Quintergy Antilles
- 1988: Standards Antilles
- 1992: Vivian Concord
- 1992: Let’s Hang Out Verve
- 1994: Carnegie Hall Salutes the Jazz Masters Verve
- 1994: Tangence (with the Robert Farnon Orchestra) Verve
- 1996: The Brass Orchestra Verve
- 1998: Heroes Verve
With Kai Winding as co-leader
- 1954: Jay and Kai (Savoy)
- 1954: An Afternoon at Birdland
- 1954: Jay and Kai (Prestige)
- 1955: K + J.J. (Bethlehem)
- 1955: ‘Nuf Said (Bethlehem)
- 1956: Trombone for Two (Columbia)
- 1956: Jay and Kai (Columbia)
- 1956: Jay and Kai + 6 (Columbia)
- 1960: The Great Kai & J. J. (Impulse!)
- 1968: Israel (A&M/CTI)
- 1968: Betwixt & Between (A&M/CTI)
- 1969: Stonebone (A&M/CTI (Japan))
As sideman
With Cannonball Adderley
- Julian “Cannonball” Adderley (EmArcy, 1955)
With Nat Adderley
- Sayin’ Somethin’ (Atlantic, 1966)
With Count Basie
- Basie Jam (1973)
- Count Basie with Joe Turner – The Bosses (1973)
- Count Basie- Kansas City 7 (Pablo, 1980) Pablo
With Kenny Burrell
- Night Song (Verve, 1969)
With Miles Davis
- The Birth of the Cool (Capitol, 1949)
- Walkin’ (Prestige, 1954)
With Paul Desmond
- Summertime (A&M/CTI, 1968)
With Kenny Dorham
- Afro-Cuban (Blue Note, 1955)
With Dizzy Gillespie
- Dee Gee Days: The Savoy Sessions (Savoy, 1951-52 [1976])
- Afro (Norgran, 1954)
- Dizzy and Strings (Norgran, 1954)
- Perceptions (Verve, 1961) – composer and arranger
With Benny Golson
- The Modern Touch (Riverside, 1957)
With Coleman Hawkins
- The Hawk Flies High (1957)
With Milt Jackson
- Bebop (East West, 1988)
With Elvin Jones
- And Then Again (Atlantic, 1965)
With Oliver Nelson
- Happenings with Hank Jones (Impulse!, 1966)
With Chico O’Farrill
- Nine Flags (Impulse!, 1966)
With Sonny Rollins
- Sonny Rollins, Vol. 2 (Blue Note, 1957)
With Moacir Santos
- Carnival of the Spirits (Blue Note, 1975)
With Lalo Schifrin
- New Fantasy (Verve, 1964)
- Once a Thief and Other Themes (Verve, 1965)
With Horace Silver
- The Cape Verdean Blues (Blue Note, 1965)
With Steve Turre
- Steve Turre (Verve, 1996)
Soundtracks
- Across 110th Street (c. 1972) Rykodisc 10706
- Willie Dynamite – Original Motion Picture Soundtrack (1974) Hip-O Select B000362202
- Cleopatra Jones – Original Motion Picture Soundtrack to (1974) Warner Bros. B00005B471