Freneau's father was a French Huguenot wine merchant, whose family settled in America after fleeing religious persecution in France. His mother was Scottish. Freneau was born in New York City and grew up in New Jersey. He graduated from College of New Jersey (later Princeton College) in 1771. He was a friend and classmate of James Madison, who was an unsuccessful suitor to his sister Mary. Aaron Burr was another classmate.
While he was a student, Freneau cowrote with Hugh Henry Brackenridge (later to become a justice of the Pennsylvania Supreme Court), Father Bombo's Pilgrimage to Mecca, a satire about a clergy who is commanded by an apparition to go to Mecca after plagiarizing the work of Lucian, the Assyrian satirist who wrote in ancient Rome and Greece. The book was said to be a novel about actual events and was one of the first novels published in America. As graduating seniors, he and Brackenridge also wrote A Poem, On the Rising Glory of America for their Commencement Day. (Freneau published his own version in 1786).
In 1776, Freneau went to the West Indies (where he wrote the poems The Beauties of Santa Cruz and The House of Night), but returned within two years and acquired ownership of a privateering ship, Aurora. He served on its crew, and when a British man-of-war captured the Aurora, Freneau was held on a British prison ship for six weeks. His poem The British Prison-Ship (1780) details the harsh treatment he received aboard the ship.
Ten years later, Freneau became assistant editor of a newspaper in New York. By then, Thomas Jefferson was Secretary of State and James Madison was active in national politics. They persuaded Freneau to become editor of a weekly Democratic-Republican newspaper they were creating to counter the views of The Gazette of the United States that carried the Federalist writing of Alexander Hamilton, George Washington, and John Adams. Jefferson and Madison's National Gazette regularly lambasted the Washington administration.
Freneau's first two collections of poems were Poetry (1786) and Miscellaneous Works (1788). He also produced collections published in 1795, 1809, and 1815. He wrote such poems as The Wild Honey Suckle (1786) and The Indian Burying Ground (1787).