Harvard was born and raised in Southwark, Surrey, England, (now part of London), the fourth of nine children of Robert Harvard (1562-1625), and his wife Katherine Rogers (1584-1635), a native of Stratford-upon-Avon whose father, Thomas Rogers (1540-1611), was an associate of Shakespeare's father (both served on the borough corporation's council). His father owned a butcher shop and the Queen's Head tavern.
Harvard's father and four of his siblings died, however, in the 1625 plague - leaving John, his mother, and a younger brother Thomas. Fifteen months after Harvard's death the widow Katherine married the Reverend Thomas Allen. In July of 1635 Harvard's mother died following a third marriage. His brother Thomas died before May 5, 1637 leaving Harvard with an inheritance. During these years various legal documents including his mother's will, his father-in-law's will, a real estate lease, and a debt document describe Harvard as a 'clerk'. Being the sole survivor of a fairly well-to-do family, made even more prosperous by inheritances from his mother's re-marriages, Harvard could be justly described as a "wealthy citizen" of Charlestown, Massachusetts.