Minidoka County is a county located in the U.S. state of Idaho. As of the 2010 census, the population was 20,069. The county seat and largest city is Rupert.

Minidoka County is part of the Burley, ID Micropolitan Statistical Area.

The name Minidoka is of Dakota Sioux origin meaning "a fountain or spring of water." Minidoka was first used in 1883 as a name for the Union Pacific's Oregon Short Line, a railroad spur in the middle of the Snake River Plain. The spur later became the site of a watering station along the line. The village of Minidoka grew up next to the station. The Minidoka name was then given to a reclamation project under then President Theodore Roosevelt which included the construction of the Minidoka Dam, completed in 1904. Minidoka National Historic Site (in Jerome County) was part of the original reclamation project and hence shares the name. Minidoka County was created by the Idaho Legislature on January 28, 1913, by a partition of Lincoln County.