Seneca is an unincorporated community in Thomas County, in the state of Nebraska in the Great Plains region of the United States. The population was 33 at the 2010 census.
Seneca was established on the Chicago, Burlington and Quincy Railroad in 1888. The location of a division point on the railroad, it was for some years the largest settlement in Thomas County. The population dwindled following the closing of the railroad roundhouse; in 2014, following a dispute on the Village Board, the residents voted to disincorporate the village.