- Jan 6 Seth Ward, English mathematician and astronomer (b. 1617)
- Feb 12 Marie Louise D'Orleans, Queen consort of Spain as the first wife of King Charles II of Spain, dies at 26
- Feb 21 Isaacus Vossius, Dutch [Isaac Vos], librarian, dies
- Mar 18 John Dixwell, English judge (b. 1607)
- Apr 16 Aphra Behn, English dramatist and novelist, dies at 48
- Apr 18 George Jeffreys, 1st Baron Jeffreys of Wem/infamous judge, dies
- Apr 19 Christina, Queen of Sweden (1644-54), dies
- Jul 8 Edward Wooster, English Connecticut pioneer (b. 1622)
- Jul 27 John Graham, of Claverhouse, 1st viscount Dundee/soldier, fatally wounded at the Battle of Killiecrankie at 41
- Aug 12 Innocent XI, [Benedetto Odescalchi], Italian, Pope (1676-89), dies at 78
- Aug 21 William Cleland, Scottish poet and soldier
- Aug 28 Claude-Jean Allouez, French Jesuit missionary and explorer, dies at 67
- Nov 13 Philipp von Zesen, German poet and historian (Bescheibung of Amsterdam), dies at 70
- Nov 26 Marquard Gude, German archaeologist and classical scholar famous for his collection of Greek and Latin inscriptions, dies at 54
- Dec 29 Olfert Dapper, Amsterdam historian/geographer, buried
- Dec 29 Thomas Sydenham, English physician (b. 1624)