He was born in Alderley Edge, Cheshire, the second of four sons to John Collie and Selina Mary Winkworth. In 1870 the family moved to Clifton, near Bristol, and John was educated initially at Windlesham in Surrey and then in 1873 at Charterhouse School. The family money had been made in the cotton trade, but in 1875 the American Civil War resulted in their financial ruin when their American stock was burnt. Collie had to leave Charterhouse and transfer to Clifton College, Bristol where he realised he was completely unsuited for the classics. He attended University College in Bristol and developed an interest in chemistry.