The city is named for John James Audubon the world famous ornithologist, artist, and painter.
Audubon was laid out by the Chicago, Rock Island and Pacific Railroad, on September 23, 1878. An auction sale of town lots was held on October 15, 1878 with total sales of $6,190. The railroad was completed on December 6, 1878 and by December 16, 1878 over fifty houses, a bank, five general stores, one jewelry store, two hotels, one restaurant, three meat markets, three blacksmith shops, one harness shop, one livery stable, two coal yards, two lumber yards, one elevator, three grain dealers, and a school house were built. With the four months of rapid growth in Audubon there was already talk of moving the county seat from Exira which was 13 miles away. In 1879 the railroad built what was to become the county courthouse and leased it to the county for five years free of cost, in case the county seat was moved to Audubon. In the 1879 general election the vote approved the moving of the county seat to Audubon.
Although the railroad was responsible for starting the town, Ethelbert J. Freeman was the driving force behind the growth of Audubon. Having lived in Exira, Freeman was the agent for the sale of the railroad lands and the town lots and was one of the first people to live in Audubon. Already active in county politics he became the first mayor of Audubon and was prominent in the incorporation of the town in 1880. Freeman was half owner of the Citizens Bank, chief of the fire department, and became the manager of the waterworks built in 1882 and later manager of the electric light plant when it was built in 1891.
Audubon has been an RAGBRAI overnight stop in 1986 and 2006.