John William Draper was born May 5, 1811, in St. Helens, Lancashire, England, to John Christopher Draper, a Wesleyan clergyman, and Sarah (Ripley) Draper. He also had three sisters, Dorothy Catherine Draper (August 6, 1807 – December 10, 1901), Elizabeth Johnson, and Sarah Ripley. On June 23, he was baptized by the Wesleyan Methodist minister Jabez Bunting. His father often needed to move the family due to serving various congregations throughout England. John Wm. Draper was home tutored until 1822, when he entered Woodhouse Grove School. He returned to home instruction (1826) prior to entering University College London in 1829. While at University College London, Draper studied chemistry under the direction of Edward Turner (chemist).
On September 13, 1831, John William Draper married Antonia Caetana de Paiva Pereira Gardner (–1870), the daughter of Daniel Gardner, a court physician to John VI of Portugal and Charlotte of Spain. Antonia was born in Brazil after the royal family fled Portugal with Napoleons invasion. There is dispute as to the identity of Antonias mother. Around 1830, Antonia was sent with her brother Daniel to live with their aunt in London.
Following his fathers death in July 1831, John Williams mother was urged to move with her children to the US state of Virginia. John William hoped to acquire a teaching position at a local Methodist college.