Educated at the local school of the Oratorians, Daunou became an Oratorian himself in 1777, taught in the order's convents from 1780, and was ordained priest in 1787. During the French Revolution, he was elected to the Convention from Pas-de-Calais. He strongly opposed Louis XVI's trial, protested against the proscription of the Girondins (moderate republican party during the Revolution), was imprisoned in October 1793, but returned to the Convention in December 1794. He was the chief author of the constitution of 1795 and founder of the National Institute, which replaced the academies suppressed in 1793. After Napoleon Bonaparte's coup in 1799, he also participated in writing the constitution of the year VIII (December 1799).

Daunou was director of the national archives from 1804 to 1815. Under the Restoration he served as deputy (1819–23, 1828–34) and then as director (1830–40) of the national archives again. He wrote numerous essays and articles on French history and literature.