As leader/co-leader

• 1974: Jaco with Pat Metheny, Bruce Ditmas, Paul Bley ( Improvising Artists, 1976) – live
• 1975: Jaco Pastorius ( Epic, 1976)
• 1980–81: Word of Mouth ( Warner Bros., 1981)
• 1982: Invitation (Warner Bros., 1983) – live
• 1986: Stuttgart Aria with Biréli Lagrène (Jazzpoint/ Le Chant du Monde, 1986) ^[1]

Posthumous releases:

• Honestly - Solo Live (Jazzpoint, 1991) – recorded in 1986
• Holiday for Pans (Sound Hills, 1993) – recorded in 1980–82
• The Birthday Concert (Warner Bros., 1995) – recorded in 1981
• Golden Roads (Sound Hills, 1997) – recorded in 1986
• A Good Stitch for Golden Roads (Sound Hills, 1997) – recorded in 1986
• Punk Jazz: The Jaco Pastorius Anthology (Warner Bros./ Rhino, 2003) [2CD] – recorded in 1968–86
• The Early Years Recordings (Holiday Park, 2006) – recorded in 1969–74
• Trio of Doom with John McLaughlin and Tony Williams (Columbia, 2007) – recorded in 1979
• Legendary Demo & Live Tracks (Victor, 2008) – recorded in 1970, 1974, 1976, and 1982
• Word of Mouth Band featuring Kazumi Watanabe, Word of Mouth Band 1983 Japan Tour (Rhino, 2012) [2CD] – recorded in 1983
• Modern American Music...Period! The Criteria Sessions (Omnivore Recordings, 2014) – recorded in 1974
• Truth, Liberty & Soul ( Resonance, 2017) – live recorded in 1982
• Jaco Pastorius Bass Workshop: Jazz Concert In Martinique (Altus Jazz, 2017) – live recorded in 1984
• Tokyo 83 (2019) - Recorded at Koseinenkin Kaikan, Tokyo, Japan on May 22, 1983

As group

Weather Report

• 1975–76: Black Market (Columbia, 1976)
• 1976–77: Heavy Weather (Columbia, 1977)
• 1978: Mr. Gone (Columbia, 1978)
• 1979: 8:30 (Columbia, 1979)
• 1980: Night Passage (Columbia, 1980)
• 1981: Weather Report (Columbia, 1982) ^[1]

Posthumous compilations:

• Live and Unreleased (Columbia, 2002) [2CD]
• Forecast: Tomorrow (Columbia, 2006) [3CD & DVD-Video]
• The Legendary Live Tapes: 1978-1981 (Columbia, 2015) [4CD]

Trio of Doom
With Tony Williams and John McLaughlin

• Trio of Doom (Columbia Legacy, 2007) – recorded in 1979. posthumous release.

With Randy Bernsen:

• Music for Planets, People & Washing Machines (Amc, 1984) – 2 tracks
• Mo' Wasabi (Zebra, 1986) – 3 tracks
• Paradise Citizens (Zebra, 1988) – 1 track

With Herbie Hancock:

• Sunlight (Columbia, 1978) – 1 track
• Mr. Hands (Columbia, 1980) – 1 track

With Brian Melvin:

• 1984–85: Brian Melvin’s Nightfood, Night Food (Timeless, 1985) ^[3]
• 1985: Brian Melvin’s Nightfood, Jazz in Toulouse (Atlus, 2016) [2CD]
• 1985: Brian Melvin Trio, Standards Zone (Global Pacific, 1990)
• 1984–86 Brian Melvin’s Nightfood, Nightfood (Global Pacific, 1988) – different from 1985 album with similar title ^[4]
• 1986: Brian Melvin Trio, Jazz Street (Timeless, 1988)

With Joni Mitchell:

• 1976: Hejira ( Asylum, 1976)
• 1977: Don Juan's Reckless Daughter (Asylum, 1977)
• 1978–79: Mingus (Asylum, 1979)
• 1979: Shadows and Light (Asylum, 1980) – live ^[1]

With others:

• Manolo Badrena, Manolo (A&M, 1979)
• Little Beaver, Party Down (Cat, 1974) – recorded in 1974
• Jimmy Cliff, Cliff Hanger (CBS, 1985) – 1 track
• Cockrell & Santos, New Beginnings (A&M, 1978)
• Michel Colombier, Michel Colombier (Chrysalis, 1979)
• Santana, "Aquamarine" (Columbia Records, 1979) --1 track
• Deadline, Down by Law (Celluloid, 1985)
• Ian Hunter, All American Alien Boy (Columbia, 1976)
• Albert Mangelsdorff, Trilogue - Live! (MPS, 1977) – recorded in 1976
• Al Di Meola, Land of the Midnight Sun (Columbia, 1976) – recorded in 1975
• Pat Metheny, Bright Size Life (ECM, 1976) – recorded in 1975
• Bob Mintzer, Source (Agharta, 1982)
• Airto Moreira, I'm Fine, How Are You? (Warner Bros., 1977)
• Michel Polnareff, Coucou Me Revoilou (Atlantic, 1978)
• Flora Purim, Everyday, Everynight (Warner Bros., 1978)
• Tom Scott, Intimate Strangers (Columbia, 1978)
• Mike Stern, Upside Downside (Atlantic, 1986) – 1 track
• Tommy Strand, Tommy Strand and The Upper Hand, Featuring Jaco Pastorius (Holiday Park, 2009) – recorded in 1971
• Ira Sullivan, Ira Sullivan (Horizon, 1976) – recorded in 1975–76
• Various artists, Havana Jam 2 (Columbia, 1979) [2LP] – 3 tracks
• Various artists, Conrad Sivert Presents Jazz at the Opera House (CBS/Sony, 1983) [2LP] – recorded in 1982