The palace's deepest foundation is religious. In the late fourteenth century, Grand Duke Jogaila issued an edict donating land in Vilnius to the diocese for the residence of its first bishop, Andrzej Jastrzębiec. The building grew through the Renaissance with successive bishops adding rooms, gardens, and outbuildings. By the eighteenth century, two major fires (1737 and 1748) had badly damaged the structure. The architect Laurynas Gucevičius rebuilt it in 1750, and the function began to shift. The last Bishop of Vilnius lived here, but after Lithuania was annexed by the Russian Empire in the 1790s the building stopped serving the church and started serving whichever empire was passing through.

Napoleon entered Vilnius in late June 1812 with the Grande Armée, on his way to invade Russia. He set up here. From these rooms he received Lithuanian noblemen who hoped he would restore the Polish-Lithuanian Commonwealth, organized military units (five infantry regiments, four cavalry regiments, the National Guard of Vilnius), and conducted the administrative business of an emperor about to march on Moscow. Six months later the Grande Armée was destroyed, the survivors stumbling back through the same city in winter. Tsar Alexander I, victorious, took up the palace next. It was here, in late 1812, that General Mikhail Kutuzov was awarded Russia's highest military honor, the Order of St. George, for the campaign that broke Napoleon's invasion. The palace had hosted both ends of the same war.

Between 1824 and 1834 the imperial Russian government commissioned Vasily Stasov, the prominent St. Petersburg architect, to reconstruct the palace in the Empire style. Karol Podczaszyński supervised the local work. Stasov's neoclassical exterior is what visitors see today: the symmetrical façade, the pediment, the reserved Petersburg formality grafted onto a much older building. Through the nineteenth century the palace served as the residence of Russian governors of the Vilnius region, including Mikhail Muravyov, who earned the nickname Vesatel, The Hangman, for his brutal suppression of the 1863 Polish-Lithuanian uprising. The building Vilnius now venerates as a presidential residence was, for nearly a century, the office of the imperial occupiers.

After Lithuania declared independence in 1918, the palace housed the Foreign Ministry and the ELTA news agency until Polish forces took Vilnius in 1920 and held it for nineteen years. Lithuania's interim capital moved to Kaunas, where another presidential palace served the country until World War II. Vilnius returned to Lithuania in 1939, then suffered Soviet occupation, then Nazi occupation, then Soviet occupation again. After 1990 the building was used as a military officers' center, then handed to artists. Only in 1997, twenty-eight years ago, did it finally become what it had been proposed to be in the early 1990s: the official seat of the President of Lithuania. The first president to use it was Algirdas Mykolas Brazauskas.

The interior is more accessible than most presidential residences in Europe. Free guided tours run on weekends in Lithuanian and English. The 1.5-hectare gated park behind the building, bounded by a four- to five-meter brick wall, opens to the public on weekday evenings and weekends. The White Hall, the main reception room where heads of state are welcomed, has hosted George W. Bush in 2002, Joe Biden in 2023 alongside Lithuanian President Gitanas Nausėda before the Vilnius NATO Summit, and the centennial commemoration of the Act of Independence in 2018. When the presidential flag flies above the green roofs, you know the country's head of state is in the building or, by extension, somewhere in the city. It is the most visible signal of Lithuanian sovereignty in a building that for centuries belonged to other people's empires.