He died on 7 September 1687 at Salisbury aged 49 and was buried in St Mary's Church, Brixham, on 20 September 1687, where his mural monument survives on the north wall of the nave inscribed as follows:
- "In memory of John Upton of Lupton Esq(ui)r(e) who piously and righteously served God and his country in his private and publick station while a justice of peace and burgesse for Dartmouth in three Parliaments at his proper cost and charges. This monument was erected by his most disconsolate relict Ursula, daughter of S(i)r John Lytcott of Moulsey in the county of Surr(e)y, K(nigh)t, with whom he lived 22 years in true conjugall affection and by whom he had three sons and one daughter: the first dyed young and others, educated in the fear of the Lord and kept from the vices of youth, gave great hopes of being eminently serviceable, were early transplanted dyeing in the true Christian faith before their father who departed this life at Salisbury Sept(ember) the 7th and was here interred the 20th Anno Aetatis 49o (Anno) Domini 1687. Here also lyes ye aboves(ai)d Ursula who had been first married to George Clerke of London, Merch(an)t, by whom shee had 8 children, ob(iit) 16 Dec(embe)r 1709 An(n)o Aet(atis) 79".
On a small table below is inscribed:
- "Arthur their eldest son was born at Dublin in Ireland Febr(uary) 14th and buryed there in Mar(ch) 1666. Arthur their second son born at Lupton Jan(uary) 6th 1667 died at Kingsbridge Nov(ember) 28th was buried here 1680. John their third son born at Lupton May 17th 1668 died and was interred in Wadham Coll(ege), Oxon Dec(ember) 1686. Ursula their onely daughter born at Lupton Jan(uary)13th 1671 died in London Aug(ust) 21th (sic) and was interred here in the same grave with her father 1687"