Harding was born in Oxford. He studied trumpet at Chetham's School of Music and was a member of the National Youth Orchestra at age 13.

At age 17, Harding assembled a group of musicians to perform Pierrot Lunaire of Arnold Schoenberg, and sent a tape of the performance to Simon Rattle in Birmingham. After listening to this tape, Rattle hired Harding as an assistant to him at the City of Birmingham Symphony Orchestra for a year, from 1993 to 1994. Harding then attended the University of Cambridge, but after his first year at university, Claudio Abbado named him his assistant with the Berlin Philharmonic Orchestra.