The presidency of Thomas Jefferson began on March 4, 1801, when Thomas Jefferson was inaugurated as the 3rd president of the United States, and ended on March 4, 1809, after two terms.

During his first term, Jefferson worked to reverse his predecessor's reshaping of the federal judiciary, and the resulting dispute led to a landmark Supreme Court ruling in Marbury v. Madison in 1803. Jefferson carried out the Louisiana Purchase the same year, significantly increasing the territory of the United States, and launched the Lewis and Clark Expedition in 1804 to survey the newly acquired lands.

The First Barbary War began two months into Jefferson's presidency after he ordered the United States Navy to combat Ottoman Tripolitania and the Barbary corsairs in the Mediterranean Sea. Peace was reached in 1805.

Jefferson responded to the Burr conspiracy in his second term when his former vice president, Aaron Burr, was allegedly plotting an insurgency in East Florida, West Florida, and the Territory of Orleans. The final two years of his presidency involved trade disputes between the United States, the United Kingdom, and France in which Jefferson authorized strict embargoes banning foreign trade.

1801

March 1801 March 4 – Thomas Jefferson is inaugurated as the third president of the United States. This is the first inauguration to take place in Washington, D.C. Aaron Burr is inaugurated as vice president. Jefferson retains Samuel Dexter as Secretary of the Treasury, Benjamin Stoddert as Secretary of the Navy, and Joseph Habersham as Postmaster General. March 5 – Levi Lincoln becomes Attorney General and acting Secretary of State. Henry Dearborn becomes Secretary of War. March 8 – Jefferson holds his first Cabinet meeting. March 11 – Building regulations in Washington, D.C. are modified to make housing more affordable by lifting the requirement that houses be made of brick or stone. March 12 – Jefferson issues a pardon for David Brown, who had been convicted of sedition. March 16 – Jefferson issues a pardon for James T. Callender, who had been convicted of sedition. March 19 – Jefferson moves into the White House (then called the President's House). March 23 – Jefferson selects William Kilty as a recess appointment to be chief judge of the Circuit Court of the District of Columbia.

April 1801 April 1 Jefferson departs from Washington, D.C. for his home at Monticello. Secretary of War Henry Dearborn becomes acting Secretary of the Navy to fill the vacancy left by Benjamin Stoddert. April 3 – Jefferson selects David L. Barnes to serve on the District Court for the District of Rhode Island as a recess appointment to succeed Benjamin Bourne. April 29 – Jefferson returns to Washington from Monticello.

May 1801 May 1 – James Madison arrives in Washington to stay with Jefferson. May 2 – James Madison becomes Secretary of State. May 6 – Samuel Dexter's tenure as Secretary of the Treasury ends. May 9 – Jefferson selects Henry Potter to serve on the U.S. Circuit Court for the Fifth Circuit as a recess appointment. May 14 Yusuf Karamanli, the pasha of Tripoli, declares war on the United States. Tripoli had demanded additional payment for protection from piracy, but the United States had refused. This begins the First Barbary War. Albert Gallatin becomes Secretary of the Treasury to fill the vacancy left by Samuel Dexter. May 15 – Jefferson's Cabinet unanimously agrees that he should send a naval squadron to the Mediterranean. May 20 – Jefferson deploys ships to fight Tripoli. May 25 – Jefferson appoints William C. C. Claiborne as governor of the Mississippi Territory. May 30 – Jefferson selects Theodore Gaillard as a recess appointment to serve as chief judge of the U.S. Circuit Court for the Fifth Circuit, but Gaillard declines.

June 1801 June 1 – A naval squadron led by Richard Dale is sent to protect American commerce from Barbary pirates. June 2 – Jefferson arrives at Mount Vernon to express condolences to Martha Washington after the earlier death of her husband George Washington. June 6 – Jefferson appoints Charles Pinckney as Minister Plenipotentiary to Spain, serving concurrently alongside the incumbent David Humphreys. June 18 – The people of New Haven, Connecticut, protest following Jefferson's appointment of Samuel Bishop as collector of customs. Elizur Goodrich of the opposition Federalist Party had been appointed by President Adams, but Jefferson did not recognize the appointment. The city's predominantly Federalist population alleges that Bishop is unfit and was selected for partisan reasons. June 26 – The USS Enterprise reaches Gibraltar. June 29 – Tripoli's flagship Mashouda arrives at Gibraltar, unaware that the USS Enterprise is monitoring them.

July 1801 July 1 – Jefferson selects Dominic Augustin Hall to serve on the U.S. Circuit Court for the Fifth Circuit as a recess appointment. July 2 – The USS President, USS Essex, and USS Philadelphia arrive at Gibraltar. Richard Dale contacts Tripoli's grand admiral Murad Reis on the Mashouda to ask whether Tripoli has declared war on the United States. Murad Reis falsely tells Dale that the nations are at peace. July 4 – Jefferson holds the first public reception at the White House. July 25 – The USS Enterprise and USS President arrive at Tripoli. July 27 – Robert Smith becomes Secretary of the Navy to fill the vacancy left by Benjamin Stoddert. July 30 – Jefferson departs from Washington for his home at Monticello. July 31 – The Convention of 1800, which ended the Quasi-War between France and the United States, comes into effect after it is ratified by France.

August 1801

August 1 – The USS Enterprise defeats the Tripolitan polacca Tripoli in the action of 1 August 1801. This is the first naval battle of the First Barbary War. August 22 – Jefferson's granddaughter Virginia Jefferson Randolph is born. August 27 – Jefferson receives a letter from an American citizen in France, informing him that Spain had transferred Louisiana to France.

September 1801 September 9 – William Loughton Smith ends his tenure as Minister Plenipotentiary to Portugal. A successor is not appointed and the position will remain vacant until 1810. September 20 – Jefferson's grandson Francis W. Eppes is born. September 30 – Jefferson returns to Washington from Monticello.

October 1801 October 22 – Jefferson selects William Stephens as a recess appointment for the District Court for the District of Georgia. October 24 – The United States signs the Treaty of Chickasaw Bluffs with the Chickasaw.

November 1801 November 28 – Gideon Granger becomes postmaster general, succeeding Joseph Habersham.

December 1801 December 6 – Jefferson appoints Robert R. Livingston as Minister Plenipotentiary to France after a vacancy of approximately five years. December 7 – The 7th United States Congress convenes for its first session. December 8 – Jefferson delivers the 1801 State of the Union Address in writing, breaking with tradition of reading it personally, and it is read by the Clerk of the United States House of Representatives. Following Jefferson, no president will deliver the address in person until Woodrow Wilson in his 1913 speech. December 17 Marbury v. Madison begins when William Marbury asks the Supreme Court to compel Secretary of State James Madison to honor his appointment as a judge. Marbury was one of several judges appointed by Jefferson's predecessor, John Adams, and then disregarded by Jefferson. The United States signs the Treaty of Fort Adams with the Choctaw. December 18 – David Humphreys ends his tenure as Minister Plenipotentiary to Spain, leaving Charles Pinckney as the sole individual holding the position. December 19 – The Senate passes a resolution declaring the Convention of 1800 fully ratified. December 21 – Jefferson proclaims the Convention of 1800 between France and the United States.

1802 January 1802 January 1 Jefferson writes to the Danbury Baptists explaining his beliefs on the separation of church and state in the United States. Jefferson is gifted the Cheshire Mammoth Cheese. January 6 – Jefferson nominates recess appointments David Leonard Barnes, Dominic Augustin Hall, William Kilty, Henry Potter, and Williams Stephens to continue serving on their respective courts. January 8 – The United Kingdom and the United States negotiate American payment to British citizens per the Jay Treaty and a commission rules that the United States owes £600,000 (). January 26 – The national library of the United States, the Library of Congress, is established. January 28 – Jefferson appoints John J. Beckley as the first Librarian of Congress.

February 1802 February 6 – The United States Congress recognizes a state of war with Tripoli and authorizes merchant ships to arm themselves.

March 1802 March 8 – The Midnight Judges Act is repealed, reversing the changes John Adams had made to the federal judiciary. March 16 The United States Army is shrunk to its 1796 numbers. Authorization to form the United States Military Academy of West Point is signed into law. It is intended to train military engineers.

April 1802

April 6 The government repeals its excise taxes on several products, including whiskey. Jefferson nominates Henry Potter, his previous appointment on the Circuit Court for the Fifth Circuit, to the District Court for the Albemarle, Cape Fear & Pamptico Districts of North Carolina. April 14 – The Naturalization Act of 1802 replaces the Naturalization Act of 1798. It reduces the residency requirements for citizenship from fourteen years to five. It also allows citizenship for anyone under 21 when their parents become naturalized citizens. April 24 – Georgia cedes the Yazoo lands to the federal government. April 26 – The Senate ratifies the negotiations of the Jay Treaty with the United Kingdom. April 27 – Jefferson nominates Edward Harris to serve on the Circuit Court for the Fifth Circuit. April 28 – The USS Constellation arrives at Gibraltar. April 29 The Judiciary Act of 1802 reduces the number of Supreme Court justices to six and has each Supreme Court justice take a position as the head of a circuit court. It also relocates the Supreme Court to Washington, D.C. Annual appropriations of $7.3 million () are authorized to pay the public debt. April 30 – The Enabling Act of 1802 is signed into law, creating a path to statehood for territories organized under the Northwest Ordinance.

May 1802 May 3 Washington, D.C. is incorporated as a city. The president is granted the power to appoint the Mayor of Washington DC. Edward Harris receives his commission for the Circuit Court for the Fifth Circuit. The 7th United States Congress adjourns from its first session. May 5 – Jefferson departs from Washington for his home in Monticello. May 30 – Jefferson returns to Washington from Monticello.

June 1802 June 16 – The United States signs the Treaty of Fort Wilkinson with the Creek people. June 17 – The USS Franklin is captured by Tripoli. June 19 – Slimane of Morocco declares war against the United States in response to its blockade of the Mashouda, which he says has been transferred to Morocco, but he retracts the declaration amid negotiations. June 30 – The United States signs two Treaties of Buffalo Creek with the Seneca people.

July 1802 July – James T. Callender begins publishing criticisms of Jefferson. Previously an ally of Jefferson, Callendar felt betrayed when he was not appointed postmaster of Richmond, Virginia. July 1 The Circuit Court for the Fifth Circuit is abolished. The nation's internal taxes are repealed. July 4 – The U.S. Military Academy at West Point opens. July 10 – The United Kingdom ratifies the negotiations of the Jay Treaty. July 15 – The negotiations of the Jay Treaty enter into force. July 21 The USS Adams arrives at Gibraltar. Jefferson departs Washington for Monticello.