Rupert is the county seat and largest city of Minidoka County, Idaho, United States. It is part of the Burley Micropolitan Statistical Area. Th…Rupert is the county seat and largest city of Minidoka County, Idaho, United States. It is part of the Burley Micropolitan Statistical Area. The population was 6,082 at the 2020 census, up from 5,554 in 2010.