February 1 – Sarsa Dengel succeeds his father Menas as Emperor of Ethiopia.
February 18 – Francis, Duke of Guise, is assassinated while besieging Orléans.
March 19 – Edict of Amboise signed at the Château d'Amboise by Catherine de' Medici, acting as regent for her son Charles IX of France, having been negotiated between the Huguenot Louis, Prince of Condé, and Anne, duc de Montmorency, Constable of France. It accords some toleration to the Huguenots, especially to aristocrats. It officially ends the first phase of the French Wars of Religion and the combined Huguenot and royal armies then march north to besiege the English in Le Havre.
May 30 – At Bornholm, the Danish fleet fires on the Swedish navy, leading to a Danish defeat and precipitating the Northern Seven Years' War.
July 28 – The English surrender Le Havre to the French after a siege.
August 13 – Northern Seven Years' War: War against the Kingdom of Sweden is declared by Denmark–Norway and the Free City of Lübeck.
September 4 – Northern Seven Years' War: King Frederick II of Denmark, advancing from Halland, takes Älvsborg fortress from Sweden.
December 4 – The Council of Trent (opened December 13, 1545) officially closes. It reaffirms all major Roman Catholic doctrines, and declares the Deuterocanonical books of the Old Testament to be canonical, along with the rest of the Bible. Chapter 1, Session 24, promulgates the decree Tametsi, stipulating that for a marriage to be valid, consent (the essence of marriage) as expressed in the vows has to be given publicly before witnesses, one of whom has to be the parish priest.
Elizabeth College, Guernsey founded under the orders of Queen Elizabeth I
January – Penelope Blount, Countess of Devonshire, English noblewoman (d. 1607)
Johann Christoph von Westerstetten, German bishop (d. 1637)
Martin Becanus, Belgian Jesuit priest (d. 1624)
January 19 – Leonhard Hutter, German theologian (d. 1616)
January 29 – William Slingsby, English army officer (d. 1634)
January 30 – Franciscus Gomarus, Dutch theologian (d. 1641)
March 5 – John Coke, English politician (d. 1644)
March 29 – Sir Miles Sandys, 1st Baronet, English politician (d. 1645)
April 15 – Guru Arjan Dev, fifth Sikh leader (A. 1606)
May 9 – Frederick IV of Fürstenberg, German noble (d. 1617)
June 1 – Robert Cecil, 1st Earl of Salisbury, English statesman and spymaster (d. 1612)
June 15 – George Heriot, Scottish artist (d. 1624)
July 19 – Lamoral, 1st Prince of Ligne (d. 1624)
September 4 – Wanli Emperor of China (d. 1620)
September 15 – Elisabeth of Anhalt-Zerbst, Electress of Brandenburg (d. 1607)
September 18 – Agnes of Limburg-Styrum, Abbess of Elten, Vreden, Borghorst and Freckenhorst (d. 1645)
September 21 – Henri, Duke of Joyeuse, French general (d. 1608)
September 27 – Thomas Freke, English politician (d. 1633)
September 30 – Enno III, Count of East Frisia, Count of Ostfriesland from 1599 to 1625 from the Cirksena family (d. 1625)
October 4 – Dorothea of Saxony, Duchess of Brunswick-Wolfenbüttel (d. 1587)
October 13 – Francis Caracciolo, Italian Catholic priest (d. 1608)
October 14 – Jodocus Hondius, Flemish artist (d. 1633)
October 28 – Berlinghiero Gessi, Italian cardinal (d. 1639)
October 30 – Sophie of Brunswick-Lüneburg, Margrave of Brandenburg-Ansbach and Brandenburg-Kulmbach, Duchess of Hunters Village (d. 1639)
November 5 – Countess Anna of Nassau, Countess of Nassau (d. 1588)
November 8 – Henry I, Duke of Lorraine (d. 1624)
November 19 – Robert Sidney, 1st Earl of Leicester, English statesman (d. 1626)
November 20 – Sophie of Württemberg, German noble (d. 1590)
November 28 – Hosokawa Tadaoki, Daimyo (d. 1646)
December 2 – Mutio Vitelleschi, Superior General of the Society of Jesus (d. 1645)
December 19 – Lord William Howard (d. 1640)
December 20 – Juan Fernandez Pacheco, 5th Duke of Escalona, Spanish noble and diplomat (d. 1615)
Yi Su-gwang, Korean scholar (d. 1628)
Charles Blount, 1st Earl of Devonshire (d. 1606)
John Dowland, English composer (d. 1626)
Michael Drayton, English poet (d. 1631)
Scipione Gentili, Italian legal scholar (d. 1616)
Anna Guarini, Italian virtuoso singer (d. 1598)
Hosokawa Gracia, Japanese noblewoman (d. 1600)
Marcin Kazanowski, Polish nobleman (d. 1636)
Zygmunt Kazanowski, Polish nobleman (d. 1634)
Robert Naunton, English politician and writer (d. 1635)
Joshua Sylvester, English poet (d. 1618)
Jean Titelouze, French organist and composer (d.1633)
Louise Bourgeois Boursier, French Royal midwife (d. 1636)
Heo Nanseolheon, Korean poet (d. 1589)
February 1 – Emperor Menas of Ethiopia (fever) (b. 1559)
February 24 – Francis, Duke of Guise, French soldier and politician (shot) (b. 1519)
March 24 – Hosokawa Harumoto, Japanese military leader (b. 1514)
March 28 – Heinrich Glarean, Swiss music theorist (b. 1488)
May 21 – Martynas Mažvydas, author of the first printed book in Lithuanian (b. 1510)
?June – Elizabeth Seymour, Marchioness of Winchester, English noblewoman (b. 1513)
June 6 – Ikeda Nagamasa, Japanese military commander (b. 1519)
June 9 – William Paget, 1st Baron Paget, English statesman (b. 1506)
August 11 – Bartolomé de Escobedo, Spanish composer (b. 1500)
August 18 – Étienne de La Boétie, French judge and writer (b. 1530)
September 17 – Henry Manners, 2nd Earl of Rutland, English soldier (b. 1526)
November – Ioan Iacob Heraclid, ruler of Moldavia (b. 1511)
December 29 – Sebastian Castello, French theologian (b. 1515)
date unknown – Odet de Selve, French diplomat (b. c. 1504)
Year 1563 (MDLXIII) was a common year starting on Friday (link will display the full calendar) of the Julian calendar.