Pepper, youngest of three children, was born in Campbell River, British Columbia, Canada, the son of a retired lumberjack. When Pepper was five years old, his family set sail in a homemade ship, navigating through the South Pacific islands for five years. His education was completed in both public schools and correspondence courses. Due to the lack of television as entertainment, the family used sketch acting as a means of fun. When the family had finished their travels, they returned to Canada and set up a shop on Denman Island off Vancouver Island.

He is best known for his role as the Christian sniper Private Daniel Jackson in Saving Private Ryan; as prison guard Dean Stanton in The Green Mile; as Frank Slaughtery in Spike Lee's 25th Hour; as journalist Joseph L. Galloway in We Were Soldiers; his leading role in the film Battlefield Earth; his depiction of Roger Maris in Billy Crystal's HBO film 61*; as Dale Earnhardt in the ESPN produced film 3: The Dale Earnhardt Story; and as Dan Morris in the film Seven Pounds, with a role alongside Will Smith. He appeared in the Jagged Edge music video "Goodbye". Most recently, Pepper provided the voice for Alex Mercer, the protagonist of the video game Prototype and the voice for Corporal Dunn, a character in the video game Call of Duty: Modern Warfare 2.

Pepper won the Razzie Award for Worst Supporting Actor for his performance in Battlefield Earth: A Saga of the Year 3000. He has stated that, had he known he was going to win the award in advance, he would have gladly accepted it in person. Pepper will star in the psychological thriller Frost Road, directed by Call of Duty creator Keith Arem.

Pepper has been married to his wife Cindy since November 1997. They have one daughter, named Annaliese, born on June 17, 2000. Pepper became an American citizen in 2008.

Broadcast Film Critics Association Awards

DVD Exclusive Awards

Emmy Awards

Genie Awards

Golden Globe Awards

Independent Spirit Awards