Thomas Jefferson's tenure as the third president of the United States began on March 4, 1801, and ended on March 4, 1809. Jefferson assumed the office after defeating incumbent president John Adams in the 1800 presidential election. The election was a political realignment in which the Democratic-Republican Party swept the Federalist Party out of power, ushering in a generation of Jeffersonian Republican dominance in American politics. After serving two terms, Jefferson was succeeded by Secretary of State James Madison, also of the Democratic-Republican Party.

Jefferson took office determined to roll back the Federalist program of the 1790s. His administration reduced taxes, government spending, and the national debt, and repealed the Alien and Sedition Acts. In foreign affairs, the major developments were the acquisition of the gigantic Louisiana Purchase from France in 1803, an embargo against trade with both Great Britain and France, and worsening relations with Britain as the United States tried to remain neutral in the midst of the Napoleonic Wars that engulfed Europe. He established a military academy, used the Navy to protect merchant ships from Barbary pirates in North Africa, and developed a plan to protect U.S. ports from foreign invasion by the use of small gunboats (a plan that proved useless when war came in 1812). He also authorized the Lewis and Clark Expedition to explore the Louisiana Territory and the Pacific Northwest.

During his second term, Jefferson's attention was focused on the trial of then former Vice President Aaron Burr for treason, which resulted in an acquittal, and on the issue of slavery, specifically the importation of slaves from abroad. In 1806, he denounced the international slave trade as a "violation of human rights" and called upon Congress to criminalize it. Congress responded by approving the Act Prohibiting Importation of Slaves the following year. Rising tensions between the United States and Britain dominated the final years of Jefferson's second term, as the Royal Navy began impressing sailors from American ships and attacking American shipping. Jefferson rejected war and instead used economic threats and embargoes that ultimately hurt the U.S. more than Britain. The disputes with Britain continued after Jefferson left office, eventually leading to the War of 1812.

Despite the economic and political troubles caused by naval tensions with Britain, Jefferson was succeeded by his preferred successor in the form of James Madison. His legacy remained highly influential until the American Civil War, but his reputation has ebbed and flowed since then. Nonetheless, in surveys of academic historians and political scientists, Jefferson is consistently ranked as one of the nation's most esteemed presidents.

Jefferson ran for president in the 1796 election as a Democratic-Republican, but finished second in the electoral vote to Federalist John Adams; under the laws then in place, Jefferson's second-place finish made him the Vice President of the United States. Jefferson strongly opposed the Federalist program, including the Alien and Sedition Acts, and the nation became increasingly polarized. Jefferson and Adams were once again the major presidential candidates of their respective parties in the 1800 presidential election, and Aaron Burr was the Democratic-Republican Party's vice presidential nominee. Adams's campaign was weakened by unpopular taxes and vicious Federalist infighting over his actions in the Quasi-War. The Democratic-Republicans accused the Federalists of being secret monarchists, while the Federalists charged that Jefferson was a godless libertine in thrall to the French.

Under the election system in place at the time, the members of the Electoral College were permitted to vote for two names for president; any tie would be decided in a contingent election in the United States House of Representatives. Jefferson and Burr each received 73 electoral votes, while Adams finished in third place with 65 votes. The House of Representatives, still controlled by the Federalists, held a contingent election in February 1801 to decide whether Jefferson or Burr would accede to the presidency. Though some Federalists preferred Burr, Federalist leader Alexander Hamilton strongly preferred Jefferson. On the thirty-sixth ballot of the contingent election, enough Federalist congressmen abstained from the vote to allow Jefferson to win the presidency. Jefferson regarded his victory as "America's Second Revolution," and he hoped to transform the country by limiting government and weakening the power of elites.

Before Jefferson could take office, there was a transition period in which he was the president-elect following his victory in the contingent election. The transition between Adams and Jefferson represented the first transfer of the presidency between two different political parties in United States history,^a and set the precedent for all subsequent inter-party transitions. It was the first time in United States history that a president handed over the presidency to a political opponent.

Unlike modern-day presidential transitions, the transitions at this time were informal affairs, with relatively minimal activity required of the president-elect.