- Jan 7 Feodor I (Fyodor/Theodore Ivanovich), Tsar of Russia (1584-98), dies at 40
- Jan 8 Johan Georg, Elector of Brandenburg (1571-91), dies at 72
- Jan 9 Jasper Heywood, English translator (b. 1553)
- Jan 17 Fyodor I Tsar of Russia (b. 1557)
- Feb 10 Anna van Bull, 1st wife of Polish/Swedish king Sigismund II, dies
- May 3 Anna Guarini, Italian singer (b. 1563)
- Jun 28 Abraham Ortelius, Flemish cartographer and dealer in maps, books, and antiquities (Theatrum orbis terrarum), dies at 71
- Aug 4 William Cecil, 1st baron Burghley, English statesman, dies at 77
- Sep 13 Philip II, King of Spain (1556-98), dies at 71
- Sep 15 Hidejoshi, [Hijoshi], Japanese general strategist/kampaku, dies
- Sep 18 Toyotomi Hideyoshi, Japanese warlord (b. 1536)
- Sep 29 Floris I van Pallandt, earl of Culemborg, dies at about 61
- Oct 11 Joachim Camerarius, German botanist (horticulture catalog) and physician, dies at 63
- Dec 6 Elbertus Leoninus, Dutch lawyer/politician, dies at about 78
- Dec 15 Philip van Marnix, Flemish ruler of St Aldegonde/poet, dies at 58
- Dec 16 Yi Sun-sin, Korean Naval Commander, shot at the naval Battle of Noryang at 53