Kanapaha Middle School is located on the west side of Alachua County within the city limits. The school was built in 1994.  It serves grade levels 6-8. 

Kanapaha describes an area within the Arredonda Grant which marked the southern end of the Florida Cotton Belt.  The word is thought to be Timucuan for palmetto leaves and house, and is apparently a reference to the thatched dwellings of the indigenous peoples of the Potano province (presently Alachua County).