Apted married Paige Simpson, his third wife, in January 2014. Apted was divorced from his second wife of ten years, the screenwriter Dana Stevens, with whom he had a son, John. From his first marriage to Jo, he had two sons, Paul and Jim. Paul Apted was a sound editor who worked on movies such as "The Wolverine"; he died from colon cancer in 2014. In 2007 Apted became a father for the fourth time to a girl, Lily Mellis Apted, who lives with her mother Tania Mellis.