Waukon Township was organized in 1880, and was named for the Dakota language word meaning "spiritual" or "sacred".

[3] According to the United States Census Bureau, the township has a total area of 36.2 square miles (93.7 km2), all land.

The racial makeup of the township was 96.60% White, 2.04% Native American, and 1.36% from two or more races.

23.3% of all households were made up of individuals, and 8.3% had someone living alone who was 65 years of age or older.

There were 8.7% of families and 9.1% of the population living below the poverty line, including no under eighteens and 22.2% of those over 64.