Waubay is a city in Day County, South Dakota, United States. The population was 473 at the 2020 census. Waubay had its start in the e…Waubay is a city in Day County, South Dakota, United States. The population was 473 at the 2020 census. Waubay had its start in the early 1880s when the railroad was extended to that point. The school district is Waubay Public 18-3. The local newspaper is the oldest business in town, called the Waubay Clipper.