Williamson died at Cobham, Kent, on 3 October 1701, and was buried in Westminster Abbey, where his widow joined him a year later. He had become very rich by taking advantage of the many opportunities of making money which his official position gave him; and despite the heavy debts left by her brother, his wife is also said to have brought him a fortune. He left £6,000 and his library to Queen's College, Oxford; £5,000 to found a school at Rochester, Sir Joseph Williamson's Mathematical School; and £2,000 to Thetford. A great number of Williamson's letters, dispatches, memoranda, etc., are among the English state papers.