Starting as the capital of the county of Geneva, after the demise of the counts of Geneva, it became integrated into the House of Savoy's possessions in 1401. In 1444, it was set up by the Princes of Savoy as the capital of a region covering the possessions of the Genevois, Faucigny and Beaufortain. With the advance of Calvinism in 1535, it became a center for the Counter-Reformation and the bishop's see of Geneva was transferred here. After being suppressed in 1801, it was restored in 1822.
During the French Revolution the Savoy region was conquered by France. Annecy became attached to the département of Mont Blanc, of which the capital was Chambéry. After the Bourbon Restoration in 1815, it was returned to the Kingdom of Sardinia (heir of the Duchy of Savoy). When Savoy was sold to France in 1860, it became the capital of the new département of Haute-Savoie.
Annecy was the site of the second round of General Agreement on Tariffs and Trade (GATT) talks in 1949.
In 2012, a multiple murder occurred in the Annecy area.