Born in Estagel, France, Arago was educated at the Ecole Polytechnique in Paris and then spent some years in Spain, where he accompanied Jean Baptiste Biot on a measurement of an arc of meridian. On his return to Paris in 1809 he was elected to the Académie des Sciences and received the chair of analytical geometry at the Ecole Polytechnique. In 1830 he succeeded J. B. J. Fourier as the permanent secretary of the Ecole Polytechnique. Arago worked in a number of branches of physics.

His first investigations concerned the polarization of light and in 1811 he discovered chromatic polarization. He was a vigorous defender of A. J. Fresnel's wave theory of light against the criticisms of Laplace and Biot, who both supported the corpuscular theory. In 1838 he described an experiment to decide the issue by comparing the speed of light in air with that in a denser medium. Shortly before Arago's death, Léon Foucault and Armand Fizeau proved that the experiment supported the wave theory.

Arago also worked on electromagnetism, showing that a coil of wire carrying a current could act as a magnet. He also found that a rotating copper disk could deflect a magnetic needle suspended above it. (This arrangement, known as Arago's disk, depends on magnetic induction.)

In astronomy, Arago discovered the Sun's chromosphere. He also played a part in the discovery of Neptune by Urbain Leverrier.

Arago was a fierce republican and, from 1830 onward, he was involved in political life as deputy for the Pyrenées Orientales. In 1848 he became a government minister and, among other measures, abolished slavery in the French colonies.