Minidoka County is a county located in the U.S. state of Idaho. As of the 2020 census, the population was 21,613. 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.