Nathan Clifford was born of old Yankee stock in Rumney, New Hampshire to a farmer and his wife, the only son of seven children (His great-great-grandmother, Ann Smith, wife of Israel Clifford, was the accuser of Goody Cole.) He attended the public schools of that town, then the Haverhill Academy in New Hampshire, and finally the New Hampton Literary Institute. After teaching school for a time, he studied law in the offices of Josiah Quincy and was admitted to the bar in Maine in 1827, establishing his first practice in Newfield, Maine.

He served in the Maine House of Representatives from 1830 to 1834 and served as Speaker of that house the last two years. He was then Maine Attorney General from 1834 until 1838, when he was elected as a Democrat to the 26th and 27th Congresses, serving March 4, 1839 through March 3, 1843, and representing the Second and then the Third District. He was not a candidate for re-election in 1842.

In 1846, President James K. Polk appointed him 19th Attorney General of the United States. Clifford served in Polk's Cabinet from October 17, 1846, to March 17, 1848. Immediately after completing his service with the Justice Department he became the U.S. Envoy Extraordinary and Minister Plenipotentiary to Mexico, serving from March 18, 1848 to September 6, 1849. It was through Clifford that the Treaty of Guadalupe Hidalgo was arranged with Mexico, by which California became a part of the United States.

Following his service in the diplomatic corps, Clifford resumed the practice of law in Portland, Maine.

In 1858, James Buchanan appointed him an Associate Justice of the Supreme Court of the United States. He was confirmed by a narrow margin of 26 votes to 23 in the Senate. Senators were hesitant about placing a pro-slavery Democrat on the Supreme Court. His specialties were commercial and maritime law, Mexican land grants, and procedure and practice. Though he rarely declared any legal philosophy about the Constitution, Justice Clifford believed in a sharp dividing line between federal and state authority. His major constitutional contribution may have been his dissent in Loan Association vs. Topeka (20 Wallace 655) in which he set aside "natural law," or any ground other than clear constitutional provision, from the court's reasoning in striking down legislative acts. Justice Clifford's opinions were comprehensive essays on law. Justice Clifford wrote the majority opinion of the Supreme Court in 398 cases. He served on the Court for 23 years, beginning in January 28, 1858, and continuing until his death from the complications of a stroke.

Clifford was president of the Electoral Commission convened in 1877 to determine the outcome of the U.S. presidential election, 1876. Clifford voted for Samuel Tilden (a fellow Democrat), but Rutherford B. Hayes famously won by a single vote in the Compromise of 1877.

Clifford died in Cornish, Maine in 1881; he was interred in Evergreen Cemetery, in Portland, Maine. The Nathan Clifford Elementary School in Portland is named for him.

Clifford's son William Henry Clifford was a successful lawyer and an unsuccessful candidate for the Maine State House of Representatives; his grandson, another Nathan Clifford was also a lawyer and briefly president of the Maine State Senate.