The son of a Lutheran pastor from Hamburg, Encke was educated at Göttingen where he impressed Karl Gauss. In 1816 he was appointed to the staff of the Seeberg Observatory, Gotha, where he remained until 1825 when he moved to the Berlin Observatory as its director.

A faint comet had first been observed by P. Mechain in 1786. Over the years other reports were made in 1795, 1805, and 1818 of a series of faint comets. Although several astronomers suspected there was only one comet involved, it was Encke who provided in 1819 the necessary computations. He showed that Encke's comet, as it became known, had a period of 3.3 years and predicted that it would be at perihelion again on 24 May 1822. His prediction was accurate to within a few hours and Encke thus became, after Halley, only the second man to predict the return of a periodic comet successfully.