Howard was born in North London, either in Hackney or Enfield. His father, also John, was a wealthy upholsterer at Smithfield Market in the city. His mother Ann Pettitt died when he was five years old, and, described as a "sickly child", he was sent to live at Cardington, Bedfordshire, some fifty miles from London, where his father owned property. His father, a strict disciplinarian with strong religious beliefs, sent the young John to a school in Hertford and then to John Eames's dissenting academy in London.