|Covid-19|January – King Philip II of Spain marries his third wife, 14-year-old Elisabeth of Valois.
January 15 – Elizabeth I of England is crowned in Westminster Abbey.
February 27 – Queen Elizabeth I of England establishes the Church of England, with the Act of Uniformity 1558 and the Act of Supremacy 1558. The Oath of Supremacy is reinstated.
March 23 – Emperor Gelawdewos of Ethiopia, defending his lands against the invasion of Nur ibn Mujahid, Sultan of Harar, is killed in battle. His brother Menas succeeds him as king.
April 2–April 3 – Peace of Cateau Cambrésis: France makes peace with England and Spain, ending the Italian War of 1551–59. France gives up most of its gains in Italy (including Savoy), keeping only Saluzzo, but keeps the three Lorraine bishoprics of Metz, Toul, and Verdun, and the formerly English town of Calais.
May 2 – John Knox returns from exile to Scotland to become the leader of the beginning Scottish Reformation.
May 13 – At Basel, the body of Dutch Anabaptist leader David Joris is exhumed and burned, following his posthumous conviction of heresy.
June 2 – A royal edict in France makes heresy punishable by death.
July 10 – Francis II becomes King of France following the death of his father, Henry II, in a jousting accident.
August 15 – Led by Don Tristán de Luna y Arellano, a Spanish missionary colony of 1,500 men, on 13 ships, arrives from Vera Cruz at Pensacola Bay, founding the oldest European settlement in the mainland U.S. (St. Augustine is founded in 1565.)
September 4 – Establishment of Gorkha state by Dravya Shah beating local Khadka kings, which is the origin of current country Nepal.
September 19 – Just weeks after arrival at Pensacola, the Spanish missionary colony is decimated by a hurricane that kills hundreds, sinks five ships, with a galleon, and grounds a caravel; the 1,000 survivors divide to relocate/resupply the settlement, but suffer famine & attacks, and abandon the effort in 1561.
September 21 – The 15-year-old King Francis II of France is crowned at Reims. The crown is too heavy for him and has to be held in place by his nobles.
December 25 – Pope Pius IV succeeds Pope Paul IV as the 224th pope.
University of Geneva is founded by John Calvin.
Oda Nobunaga wins control of his native province of Owari.
Margaret of Parma becomes Governor of the Netherlands in place of her brother, King Philip II of Spain.
Jean Nicot, French ambassador to Portugal 1559–61, describes the medicinal properties of tobacco which he introduces in the form of snuff to the French court.
Pope Paul IV promulgates the Pauline Index, an early version of the Index Librorum Prohibitorum.
Between 1559 and 1736 almost 1,000 people accused of being witches are executed in England.
January 1 – Virginia Eriksdotter, Swedish noble (d. 1633)
January 8 – William Helyar, Chaplain (d. 1645)
January 25 – Aleixo de Menezes, Roman Catholic archbishop (d. 1617)
February 7 – Catherine de Bourbon, daughter of Queen Joan III and King Anthony of Navarre (d. 1604)
February 18 – Isaac Casaubon, French-born classical scholar (d. 1614)
February 19 – Philip II, Margrave of Baden-Baden (d. 1588)
February 21 – Nurhaci, Chinese emperor (d. 1626)
March 12 – Christoph Brouwer, Dutch historian (d. 1617)
March 16 – Amar Singh I, eldest son and successor of Maharana Pratap of Mewar (d. 1620)
March 26 – Wolf Dietrich Raitenau, Salzburg (d. 1617)
May 4 – Alice Spencer, Countess of Derby, Baroness Ellesmere and Viscountess Brackley (d. 1637)
Stanisław Radziwiłł, Grand Marshal of Lithuania (d. 1599)
Johann Georg Gödelmann, German demonologist (d. 1611)
July 22 – Lawrence of Brindisi, Italian saint (d. 1619)
July 27 – Countess Palatine Barbara of Zweibrücken-Neuburg and by marriage Countess of Oettingen-Oettingen (d. 1618)
August 18 – Frederik van den Bergh, soldier in the Eighty Years' War (d. 1618)
September 12 – Cigoli, Italian painter (d. 1613)
September 15 – Edmond Richer, French theologian (d. 1631)
October 12 – Jacques Sirmond, French scholar and Jesuit (d. 1651)
November 11 – Tokuhime, Japanese noble (d. 1636)
November 12 – Yaza Datu Kalaya, Crown Princess of Burma (d. 1603)
November 13 – Al-Mansur al-Qasim, Imam of Yemen (d. 1620)
November 15 – Albert VII, Archduke of Austria, Governor of the Low Countries (d. 1621)
December 14 – Lupercio Leonardo de Argensola, Spanish writer (d. 1613)
Francesco Bassano the Younger, Italian painter (d. 1592)
Catherine de Bourbon, sister of Henry IV of France (d. 1604)
George Chapman, English dramatist (d. 1634)
Ikeda Motosuke, Japanese military commander (d. 1584)
John Penry, Welsh Protestant martyr (d. 1593)
Honinbo Sansa, Japanese player of Go (d. 1623)
John Spenser, president of Corpus Christi College, Oxford (d. 1614)
January – Christina Gyllenstierna, leading opponent of King Christian II of Denmark and Norway
January 1 – King Christian III of Denmark and Norway (b. 1503)
January 25 – King Christian II of Denmark, Norway and Sweden (b. 1481)
February 12 – Prince-elector Otto Henry of the Palatinate (b. 1502)
March 8 – Thomas Tresham, English Catholic politician
March 16 – Anthony St. Leger, Lord Deputy of Ireland (b. 1496)
March 23 – Emperor Gelawdewos of Ethiopia (in battle) (b. 1522)
March 30 – Adam Ries, German mathematician (b. 1492)
July 10 – King Henry II of France (jousting accident) (b. 1519)
August 18 – Pope Paul IV (b. 1476)
September 7 – Robert Estienne, French printer (b. 1503)
September 10 – Anthony Denny, confidant of Henry VIII of England (b. 1501)
September 15 – Isabella Jagiellon, Queen of Hungary (d. 1519)
October 2 – Jacquet of Mantua, French composer (b. 1483)
October 6 – William I, Count of Nassau-Dillenburg (b. 1487)
November 5 – Kanō Motonobu, Japanese painter (b. 1476)
November 18 – Cuthbert Tunstall, English church leader (b. 1474)
November 20 – Lady Frances Brandon, claimant to the throne of England (b. 1517)
Realdo Colombo, Italian surgeon and anatomist (b. 1516)
Leonard Digges, English mathematician and surveyor (b. c. 1515)
Owen Oglethorpe, English priest
Conn O'Neill, 1st Earl of Tyrone, Irish rebel (b. 1480)
Wen Zhengming, Chinese painter (b. 1470)
Year 1559 (MDLIX) was a common year starting on Sunday (link will display the full calendar) of the Julian calendar.