In 1887 the Fremont, Elkhorn, and Missouri Valley Railroad extended its tracks from York to Hastings. Henderson was built along the railroad on land sold by Cornelius Regier to the Pioneer Town Site Company in October 1887, for $15,000. The village, named for David Henderson, an early settler in Henderson Township, became a strong community center with businesses, homes, and a school established during the first year. The first church, built in 1906, was followed within a few years by two others.
Railroad service continued to furnish the lifeblood of the town and aid its growth. Although the depression hit the area hard and the railroad decided to remove its tracks in 1941, community loyalty and resourcefulness helped overcome adversity. The development of deep well irrigation and the establishment of manufacturing plants to supply the irrigation business brought a new era of prosperity. During the 1950s and 1960s the town doubled in population, built a new hospital, a new school, and many new homes.
The energy and cooperative efforts of its people have made Henderson a landmark among small, rural Nebraska communities.