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)
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)
Tribute albums:
1979 A Tribute to John Fahey (Kicking Mule)
2006 I Am the Resurrection: A Tribute to John Fahey (Vanguard)
Friends of Fahey Tribute (Slackertone)
The Revenge of Blind Joe Death: The John Fahey Tribute Album (Takoma)
2007 The Great Koonaklaster Speaks: A John Fahey Celebration (Table of the Elements)