Henderson is a city in York County, Nebraska, United States. The population was 991 at the 2010 census. Henderson was platted in 18…Henderson is a city in York County, Nebraska, United States. The population was 991 at the 2010 census. Henderson was platted in 1887 when the Fremont, Elkhorn & Missouri Valley Railroad was extended to that point. It was named for David Henderson, a pioneer settler. Henderson was incorporated in 1899.