Niobrara is a village in Knox County, Nebraska, United States. The population was 363 at the 2020 census. Niobrara was founded in 1856, when a group of men headed by a Dr. Benneville Yeakel Shelly marked their claim to an area on the banks of the Missouri River. There, a fort was built to protect the early settlers from Indian attacks. The settlement t…Niobrara is a village in Knox County, Nebraska, United States. The population was 363 at the 2020 census. Niobrara was founded in 1856, when a group of men headed by a Dr. Benneville Yeakel Shelly marked their claim to an area on the banks of the Missouri River. There, a fort was built to protect the early settlers from Indian attacks. The settlement took its name from the Niobrara River.