In 1804, Lewis and Clark held council with the local tribes on a nearby bluff and called the area Council Bluff.

The Mormons--bound for Utah--first arrived here in the 1840s and named the place Kanesville. Over the next few years, the community became an important way station for the Mormon faithful. As westward travel over the trail on the north side of the Platte increased, this area became one of the more popular jumping-off places. Mormon population in the community reached its peak in 1848, but there were still several thousand here in 1852, when word came that all the Latter-day Saints should go on to Salt Lake City. After the last of the Mormons departed, Kanesville was for a time without government, because the Mormons church was the only government the town had. The remaining inhabitants re-adopted the name of Council Bluffs.

In 1863 the town was chosen as the eastern terminus of the Union Pacific railroad. Actual construction of the railroad to the West was begun in 1866. By 1870 five railroads had made connections with the Union Pacific here.