1981 Live in Tasmania (Takoma)
1998 Georgia Stomps, Atlanta Struts and Other Contemporary Dance Favorites (Table of the Elements)
2003 Hard Time Empty Bottle Blues (Table of the Elements)
2004 The Great Santa Barbara Oil Slick (Water/Revenant)
2005 On Air (Tradition & Moderne) Some Summer Day (Intergroove)
Compilation albums:
1969 Memphis Swamp Jam (Duets by Fahey and Bill Barth using the pseudonyms of R L Watson and Josiah Jones.)
1970 Zabriskie Point: Original Motion Picture Soundtrack (MGM)
1974 The Essential John Fahey (Vanguard)
Leo Kottke, John Fahey & Peter Lang (Takoma)
1977 The Best of John Fahey 1959–1977 (Takoma)
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 (Rhino)
1996 The Legend of Blind Joe Death (Takoma)
1996 The Best of the (Vanguard) Years (Vanguard)
1996 Death Chants, Breakdowns & Military Waltzes (Takoma)
Compilations 2004-2011; Tribute albums