He was son of Stephen Goffe, puritan rector of Bramber in Sussex, and brother of Stephen Goffe (Gough), royalist agent. His father was deprived of his living in 1605 for his part in organising the puritan petitions to James I. He began life as an apprentice to a London salter, a zealous parliamentarian. Goffe was a man of religious feeling, nicknamed "Praying William".

By his marriage with Frances, daughter of General Edward Whalley, he became connected with Oliver Cromwell's family and one of his most faithful followers. He was imprisoned in 1642 for his share in the petition to give control of the militia to the parliament.