Hughes received his B.A. from California Baptist College, his M.Div. from Golden Gate Baptist Theological Seminary, and his Ph.D. from Southern Baptist Theological Seminary, also studying at the University of Redlands.

Hughes was formerly employed at the Southern Baptist Theological Seminary in Louisville, Kentucky as Associate Vice President for External Programs and associate Professor of Communication and Mass Media. He is currently Professor of Missions and Evangelism at Clear Creek Baptist Bible College as Professor of Missions and Evangelism. He has also worked as a missionary in Africa.

Hughes' fiction tends to deal seriously with religious themes, particularly in The Fallen and its sequel The Eternity Gene. Of his non-fiction, Satan's Whispers has the distinction of having been adopted for use by the Billy Graham Evangelistic Association.

Hughes' most extended body of work consists of his two fantasy sequences about a magical country split into three states by a two-headed dragon's occupation of the mountain pass linking each region with the others. As a result, the magical potential of each region has developed differently. The "Pelmen the Powershaper" trilogy tells of the end of the dragon's reign and its consequences; The unfinished "Wizard and Dragon" sequence, also projected as a trilogy, is set earlier in the country's history and deals with how the dragon was originally created.

Hughes' powerfully imagined dragon Vicia-Heinox with its two bickering heads has set a pattern for the portrayal of similar creatures in other media, including the animated film Quest for Camelot (1998) and the public television children's program Dragon Tales (1999 onward).

Fantasy

Pelmen the Powershaper

1. The Prophet of Lamath (1979)
2. The Wizard in Waiting (1982)
3. The Power and the Prophet (1985)

Wizard and Dragon

1. The Forging of the Dragon (1989)
2. The Faithful Traitor (1992)

Science Fiction

The Fallen

• A Novel (1995)
• The Eternity Gene (1999)

Other

• Gabriel's Trumpet (1993)

Non-fiction

• Plays That'll Preach (1985)
• A Real Live Missionary (1990)
• Talking to the World in the Days to Come (1991)
• Breaking the Lies That Bind (1992)
• Questioning God (2002)