Beaver Crossing was platted in 1875 in anticipation of railroad construction, though the railroad didn't actually arrive until 1887. It's named for a nearby crossing of Beaver Creek along the Nebraska City-to-Fort Kearny trail.

An EF3 tornado struck Beaver Crossing on May 11, 2014, damaging nearly every structure in the village with no fatalities reported. Population 375 in 2020; race-car driver Jan Opperman once lived here.