1973 After the Ball (Reprise) 2003 on CD
Fare Forward Voyagers (Soldier's Choice) (Takoma) 1992 on CD (Shanachie) and 2007 (Ace)
1975 Old Fashioned Love (Takoma)
Christmas with John Fahey Vol. II (Takoma)
1979 John Fahey Visits Washington D.C. (Takoma)
1980 Yes! Jesus Loves Me (Takoma)
1982 Christmas Guitar Volume I (The New Possibility rerecorded)
1983 Railroad (Takoma)
Popular Songs of Christmas & New Year's (Varrick )
1984 Let Go (Varrick)
1985 Rain Forests, Oceans and Other Themes (Varrick)
1986 Christmas Guitar (Varrick )
1987 I Remember Blind Joe Death (Varrick)
1989 God, Time and Causality (Shanachie)
1991 The John Fahey Christmas Album
1992 Old Girlfriends and Other Horrible Memories (Varrick)
1996 Double 78
1997 City of Refuge (Tim/Kerr Records)
The Mill Pond (Double EP) (Little Brother Records)
Womblife (Table of the Elements )
The Epiphany of Glenn Jones (Thirsty Ear Records)
2000 Hitomi (LivHouse Records)
2002 John Fahey Trio, Vol. 1 (Jazzoo Records)
2003 Red Cross (Revenant)
Live albums:
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)
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)
