Doherty has an older sister and a younger sister, named Amy-Jo and Emily, respectively. His mother Jacqueline Doherty is a nurse, who recently published a book about family life with Doherty and his drug problems, called Pete Doherty: My Prodigal Son (ISBN 978-0755316083). Doherty's father, Peter Doherty Sr., is an Army officer.

After numerous attempts to convince him to start a serious rehab, in early 2005 Doherty's father decided that he was tired of broken promises and vowed never to see his son until he was clean of drugs. The sensitivity surrounding the issue became apparent in the BBC Two Arena documentary about Doherty, on 12 November 2006, which included footage of him talking about this aspect of his personal life. He was visibly upset and had to politely ask the interviewer at one point to stop filming. In October 2007, Doherty said in an interview with BBC Radio 4 show, Front Row, that he had reconciled with his father after 3 years of no contact when his father ca