|Covid-19|January – Burmese–Siamese War (1547–49): King Tabinshwehti of Burma begins his invasion of the Ayutthaya Kingdom. This ends in retreat.
February 3 – Burmese–Siamese War: Burmese viceroy Thado Dhamma Yaza I of Prome slays Sri Suriyothai, queen consort of the Ayutthaya Kingdom on her war elephant when she intervenes in battle to protect the life of her husband.
March 29 – The city of Salvador da Bahia, Brazil's first capital, is founded.
June 9 – Book of Common Prayer introduced in English churches; Prayer Book Rebellion against it breaks out in the West Country.
July – Kett's Rebellion in East Anglia, against land enclosures; rebellion in Oxfordshire against landowners associated with religious changes.
July 27 – Francis Xavier arrives in Japan.
August 8–9 – England and France declare war.
August 17 – Battle of Sampford Courtenay in England: Prayer Book Rebellion quashed.
August 26 – Battle of Dussindale in England: Kett's Rebellion quashed.
September 17 – Council of Trent prorogued indefinitely.
November 4 – The Pragmatic Sanction is proclaimed by Charles V, Holy Roman Emperor. The Seventeen Provinces are declared inseparable.
November 29 – The lengthy and large Papal conclave, 1549–50 goes into session in the Apostolic Palace in Rome to decide a successor to Pope Paul III.
Peter Canisius starts the Counter-Reformation in Bavaria.
The spire of Lincoln Cathedral in England is blown down leaving St. Olaf's Church, Tallinn, in Estonia as the World's tallest structure.
Although trade existed between the two beforehand, in this year the Portuguese begins to send regular seasonal maritime trade missions to Ming Dynasty China at Sao João Island (also known as Shangchuan Island) near Macau.
Excerpta antiqua is published by Hervagius at Basel in Switzerland.
January 26 – Jakob Ebert, German theologian (d. 1614)
January 26 – Francesco Bassano the Younger, Italian painter (d. 1592)
February 3 – Louis of Valois, French prince (d. 1550)
February 4 – Eustache Du Caurroy, French composer (d. 1609)
February 15 – Barnim X, Duke of Pomerania (1569–1603) (d. 1603)
February 20 – Francesco Maria II della Rovere, Duke of Urbino, last Duke of Urbino (d. 1631)
March 10 – Francis Solanus, Spanish missionary and saint (d. 1610)
March 11 – Hendrik Laurenszoon Spiegel, Dutch writer (d. 1612)
April 5 – Françoise d'Orléans-Longueville, French princess (d. 1601)
April 13 – Juraj IV Zrinski, Count of Croatia (d. 1603)
June 15 – Elizabeth Knollys, English noblewoman (d. 1605)
July 2 – Duchess Sabine of Württemberg, by marriage Landgravine of Hesse-Kassel (d. 1581)
July 5 – Francesco Maria del Monte, Italian Cardinal (d. 1627)
July 12 – Edward Manners, 3rd Earl of Rutland (d. 1587)
July 20 – Pierre de Larivey, French dramatist of Italian origin (d. 1619)
July 30 – Ferdinando I de' Medici, Grand Duke of Tuscany (d. 1609)
August 2 – Mikołaj Krzysztof "the Orphan" Radziwiłł, Polish nobleman (d. 1616)
August 10 – Catherine of Brandenburg-Küstrin, daughter of Margrave John of Küstrin (d. 1602)
September 1 – Charles Philippe de Croÿ, Marquis d’Havré, Belgian noble and politician (d. 1613)
October 17 – Denis Godefroy (d. 1622)
November 1 – Anna of Austria, Queen of Spain (d. 1580)
November 5 – Philippe de Mornay, French writer (d. 1623)
November 30 – Sir Henry Savile, English educator (d. 1622)
December 9 – Costanzo Antegnati, Italian composer, organist (d. 1624)
December 20 – John Petre, 1st Baron Petre, English politician and baron (d. 1613)
December 24 – Kaspar Ulenberg, German theologian (d. 1617)
Kutsuki Mototsuna, Japanese military commander (d. 1632)
John Rainolds, English scholar and Bible translator (d. 1607)
Juan de Salcedo, Spanish conquistador (d. 1576)
Marek Sobieski, Polish noble (d. 1605)
Ogawa Suketada, Japanese warlord (d. 1601)
January 28 – Elia Levita, Yiddish writer (b. 1469)
February 3 – Chief Queen Sri Suriyothai, consort of King Maha Chakkrapat of Ayutthaya (killed in battle)
February 14 – Il Sodoma, Italian painter (b. 1477)
March 10 – Thomas Seymour, 1st Baron Seymour of Sudeley, English politician and diplomat (b. 1508)
April – Andrew Boorde, English traveller (b. 1490)
April 15 – Henry Somerset, 2nd Earl of Worcester (b. 1496)
November 10 – Pope Paul III (b. 1468)
December 7 – Robert Kett, English rebel (executed)
December 21 – Marguerite de Navarre, queen of Henry II of Navarre (b. 1492)
date unknown – Daniel Bomberg, printer
María de Toledo, Vicereine and regent of the Spanish Colony of Santo Domingo (b. 1490)
Year 1549 (MDXLIX) was a common year starting on Tuesday (link will display the full calendar) of the Julian calendar. In the Kingdom of England, it was known as "The Year of the Many-Headed Monster", because of the unusually high number of rebellions which occurred in the country.