The soundtrack was composed by award-winning composer Jeremy Soule and his brother, Julian Soule. The Prey soundtrack was released in two volumes (nearly 2 hours of the game's 3-hour score). The end credits feature the song "Take Me Home" by After Midnight Project.
There are several jukeboxes in the game which allow the player to choose from a small selection of licensed songs. The full selection of songs is, in the order they are arranged:
- "Free Ride" by The Edgar Winter Group;
- "Barracuda" by Heart;
- "You've Got Another Thing Comin" by Judas Priest;
- "Cat Scratch Fever" by Ted Nugent;
- "If We Could Be" by Railer;
- "Deaf Girlfriend" by Scotch Greens;
- "Settle Up" by Seven Mary Three;
- "Machine Sex" by Sheep on Drugs;
- "Anthem for Tonight" by Halifax;
- "Human Resources" by The Countdown;
- "Forever Dead" by Soil;
- "10001110101" by Clutch;
- "The Setting Sun" by MxPx (commissioned specifically for the game)
- "(Don't Fear) The Reaper" by Blue Öyster Cult. This song cannot be chosen normally, but plays on the jukebox during the alien invasion in the same level.
In addition, radio host Art Bell lends his voice to several fictional segments of his paranormal-themed radio show, Coast to Coast AM, that play from radios throughout the game. In the segments, he talks with many callers about the various alien phenomena that occur in the game.