From the 1830s to the 1860s, the area saw a great deal of traffic due to the Mormon Trail, which passed along the north bank of the Platte River. A ferry connected the two banks of the Elkhorn River near Fremont. It was a major overland route for emigrant settlers going to the West, the military and hunters.
Fremont was laid out in 1856 in anticipation that the railroad would be extended to that site. It was named after the American explorer, politician and military official General John C. Frémont. By 1857, there were 13 log houses in the town. The Union Pacific Railroad reached the town in December 1865 becoming the first railroad into the future rail hub. Sioux City and Pacific Railroad completed track into the town in 1868 with the Elkhorn Valley Railroad arriving in 1869.
Due to the town's geographically central location, the First Transcontinental Telegraph line (1861), railroad (1865) and highway (1913) passed through or very near Fremont. Original brick portions of the "Old Lincoln Highway" are located east of Fremont, on the way to Omaha.
On January 10, 1976, in downtown Fremont, the Pathfinder Hotel exploded due to a natural gas leak in the basement. At the time the hotel was being used as apartments, mostly occupied by senior citizens. It also was a meeting place for philanthropic and business organizations, and had a drug store on the northwest corner. The explosion shattered windows around the city, and the ensuing fire killed 23 people and destroyed most of the city block of the hotel.
Fremont gained national attention in 2010 when residents approved a referendum that would ban illegal immigrants from renting and working in the town.