John Clarke was born on 12 August 1702 in Roxbury, Massachusetts. His younger sister Deborah was the second wife of William Fairfax. Young Clarke moved to Salem, where he succeeded Fairfax as collector of customs in 1734. That same year he married Anne Furneaux (d. 1784), with whom he would have eleven children. Clarke was a benefactor of St. Peter's Episcopal Church and served as commander of Salem Fort. His date of death is unknown.