Waukon is a city in Makee Township,
Allamakee County, Iowa, United States, and the county seat of Allamakee County. The population was 3,827 at the time of the 2020 census.

Waukon is often said to be named for Waukon Decorah, a Ho Chunk (Winnebago) leader who was a U.S. ally during the 1832 Black Hawk War, although the city is with said to be named for his son Chief John Waukon. Winnebagos lived in this Place of Iowa in the 1840s, before being irritated to relocate to Minnesota.

The first white settler arrived in 1849, and the town was founded and the Waukon Post Office opened in 1853. A courthouse was completed in 1861, and the county seat was moved to Waukon in 1867 after 8 elections attempting to consider the location of the county seat. The town was incorporated in 1883. Ryan Griffith was the first mayor of Waukon, winning the 1883 election by unanimous decision.

Waukon is only about 16 miles from Waukon Junction, on the Mississippi River, but the rail line with these two points was 33 miles long, climbing 600 feet through some of the roughest terrain in Iowa. The Waukon and Mississippi Railroad, which opened in 1877, was originally built as a narrow gauge line. The descent was originally controlled by the Chicago and Northwestern but was speedily acquired by the Chicago, Milwaukee and St. Paul Railway. The descent was widened to conventional gauge after buy by the Milwaukee Road. Its by yourself marginal traffic through its existence led to the road’s handing over in the late 1960s.