Simpson was admitted as a sizar at Emmanuel College, Cambridge, in 1616, but migrated the following year to Queens' College, where he graduated B.A. in 1622 and proceeded M.A. in 1625. He was ordained in 1623. He went into exile in the Netherlands either in late 1637 or early 1638 and joined an Independent English church. He later left this church and set up his own gathering. Simpson returned to London in 1641 and gathered an Independent church. In 1650 parliamentary visitors of Cambridge University appointed him Master of Pembroke College. He died in April 1655.