 Pierrepont married Elizabeth, daughter of Sir Thomas Harries, Bart., of Tong Castle, Shropshire, by whom he had five sons and five daughters.His eldest son, Robert (d. 1666), was the father of Robert Pierrepont, 3rd Earl of Kingston-upon-Hull, William Pierrepont, 4th Earl of Kingston-upon-Hull, and Evelyn Pierrepont, 1st Duke of Kingston-upon-Hull; and his third son, Gervase (1649-1715), was created Baron Pierrepont in 1701, a title which became extinct on his death.His daughter Grace married Gilbert Holles, 3rd Earl of Clare.