| Year | Album | Label |
|---|
| 1967 | Contemporary Guitar Spring 1967(Compilation with tracks by Max Ochs, John Fahey, Bukka White, Harry Taussig and Robbie Basho.) | Takoma |
| 1969 | Memphis Swamp Jam(Three guitar duets by John Fahey, and Bill Barth using the pseudonyms of R L Watson and Josiah Jones.) | |
| 1970 | Zabriskie Point: Original Motion Picture Soundtrack (Motion picture soundtrack) | MGM |
| 1974 | The Essential John Fahey | Vanguard |
| Leo Kottke, Peter Lang & John Fahey | Takoma |
| 1977 | The Best of John Fahey 1959–1977 |
| 1993 | The New Possibility: John Fahey's Guitar Soli Christmas Album/Christmas with John Fahey Vol. 1 | Rhino |
| 1994 | The Return of the Repressed: The John Fahey Anthology |
| 1996 | The Legend of Blind Joe Death | Takoma |
| 1996 | The Best of the Vanguard Years | Vanguard |
| 1996 | Death Chants, Breakdowns & Military Waltzes(Reissue of both issues of the album) | Takoma |
| 2002 | John Fahey Trio, Vol. 1 | Jazzoo |
| 2004 | The Best of John Fahey, Vol. 2: 1964–1983 | Takoma |
| Of Rivers and Religion/After the Ball | Warner Bros. |
| 2005 | On the Sunny Side of the Ocean | Brook Records |
| 2006 | Sea Changes & Coelacanths: A Young Person's Guide to John Fahey | Table of the Elements |
| 2006 | Vanguard Visionaries | Vanguard |
| 2009 | Twilight on Prince Georges Avenue: Essential Recordings | Rounder |
| 2011 | Your Past Comes Back To Haunt You: The Fonotone Years 1958–1965 | Dust-to-Digital |
| 2023 | Proofs & Refutations (Reissues Double 78 alongside new material) | Drag City |
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