Waukon is a city in Makee Township, Allamakee County, Iowa, United States, and the county seat of Allamakee County. The population was 4,131 at the 2000 census. It is home to the annual Allamakee County Fair.
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 also said to be named for his son Chief John Waukon. Winnebagos lived in this area of Iowa in the 1840s, before being forced to relocate to Minnesota.
The terrain between Waukon and the Mississippi River is the steepest along the Iowa bank of the Mississippi, and while the more gradual slopes of counties to the South attracted early, major railroad development, Waukon struggled to be served by a branch of the Chicago, Milwaukee, St. Paul and Pacific Railroad (The Milwaukee Road) starting in 1877. It ran as a branch line from Waukon Junction on the Mississippi River NW to termination in Waukon. It was originally built as a narrow gauge railroad but was converted to standard gauge after purchase by the Milwaukee Road. Its only marginal traffic through its existence led to the road's abandonment in the late 1960s.