The city of Morgan was settled in 1855, and the county was created in 1862. During the Utah War (1857-58), settlers in Milton supplied feed for the horses of Mormon troops stationed in canyon passes watching for Johnston's Army. Lot Smith of Stoddard blocked Echo Canyon, buried U.S. Army supply trains, and stampeded government horses and cattle. Despite such incidents, the "war" was settled peacefully.

Morgan has a larger percentage of privately owned land than any other county in Utah. Much of it is used for stock raising, especially beef and dairy cattle and sheep, and for hay and other field crops. Lumber was a major industry during 1860-75 in Hardscrabble Canyon. Thousands of railroad ties were furnished to build the Union Pacific Railroad line, and charcoal was shipped to Bingham for use in smelting. During the building of the UP Railroad in 1868, a number of businesses opened in Morgan City and it became the county's trade center.