Waubay is a city in Day County, South Dakota, United States.

The local newspaper is the oldest business in town, called the Waubay Clipper.

According to the United States Census Bureau, the city has a total area of 1.46 square miles (3.78 km2), all land.

The racial makeup of the city was 59.9% White, 36.5% Native American, 0.3% Asian, and 3.3% from two or more races.

The racial makeup of the city was 71.45% White, 25.23% Native American, 0.15% Pacific Islander, and 3.17% from two or more races.

34.5% of all households were made up of individuals, and 19.6% had someone living alone who was 65 years of age or older.