Peter Doherty was born in Hexham, Northumberland, England. He grew up at a number of army garrisons as a result of his Irish father Peter's work as an officer in the British Army, living at various times at garrisons in Catterick, Belfast, Germany, Bedworth, Dorset and Larnaca, along with his mother Jacqueline, a nurse of part Jewish descent, and two sisters, Amy Jo and Emily. Pete was the second of the three children. He was academically successful, achieving 5 grade A* and 6 grade A GCSEs, at Nicholas Chamberlaine Comprehensive School in Bedworth, although this has erroneously been reported as 11 grade A*s and two A grades at A Level and two other passes. At the age of 16, he won a poetry competition and embarked on a tour of Russia organised by the British Council.

After his A-levels he moved to his grandmother's flat, where he said he felt 'destined' to be, and got a job filling graves in Willesden Cemetery, although most of his time was spent reading and writing while sitting on gravestones.

He attended Queen Mary, part of the University of London, to study English literature, but left the course after his first year. After leaving university, he moved into a London flat with his friend and fellow musician Carl Barât, who had been a classmate of Pete's older sister at Brunel University.