Napi Headquarters is a census-designated place (CDP) in San Juan County, New Mexico, United States.

According to the United States Census Bureau, the CDP has a total area of 3.3 square miles (8.5 km2), all land.

There were 187 housing units at an average density of 56.8 per square mile (21.9/km2).

5.6% of all households were made up of individuals, and 0.6% had someone living alone who was 65 years of age or older.

The community of Napi Headquarters is served by Farmington Municipal Schools.