It is believed that a party of surveyors from Pennsylvania, led by George William Thompson, first explored the area around Triplett Creek in the summer of 1773. The first settlers of the area came mostly from Virginia to claim land grants for service in the Revolutionary War. Many of these people settled in fertile valleys along the Licking River and Triplett Creek. One of the first communities to develop was Farmers, located in the western part of the county on the Licking River. It was settled by Maj. Jim Brain, who established a hotel at the junction of two roads. Clearfield, located just south of Morehead, was settled by Dixon Clack in the early nineteenth century and grew around his water-powered sawmill and store. Morehead was probably the third community to be established in the county and likewise grew around a sawmill, which was operated by Jake Wilson. It became the county seat when Rowan County was founded in 1856.
By the 1860s Rowan County was made up of a scattering of small communities. Corn was the dominant crop and timbering the major industry, with logs floated down Triplett Creek and the Licking River. During the Civil War, the residents of the county were often threatened with attack by guerrillas who, on March 21, 1864, burned the new county courthouse. On June 12, 1864, Gen. John Hunt Morgan's Confederate cavalry camped near Farmers.
Although stone, coal, and timber were the county's main resources, they were not exploited in great quantities until the Elizabethtown, Lexington & Big Sandy Railroad arrived in the county in the early 1880s. The town of Farmers expanded quickly and was the largest city in the county until most of the timber was depleted around 1900. Rodburn, Eadston, and Brady also grew as lumber towns situated on the railroad. Rockville and Bluestone developed as rock quarry centers.
To serve the mining and logging operations, several small railroads were built in Rowan County. The largest was the Morehead & North Fork Railroad (later abandoned), which by 1908 connected the Chesapeake & Ohio Railroad at Morehead with Redwine in Morgan County. Numerous tributary spur lines extending from it moved products of the mills and mines to Morehead. Two other short lines in the county were the Kentucky Northern Railroad, which hauled logs from 1896 until its abandonment in 1900, and the Christy Creek Railroad, built by the General Refractories Company to haul clay from 1920 until 1948, when it was abandoned.
In the 1880s, Morehead became the central stage for a notorious conflict known as the Rowan County War (aka the Martin-Tolliver-Logan Feud). During a number of skirmishes for the next few years, at least 20 people were killed and possibly 100 were wounded. Beginning with an election-day barroom brawl, several gunfights took place in Morehead and the surrounding countryside. Eventually, a group led by Craig Tolliver seized political control of the town and installed allies in the county Sheriff's office and the county attorney's office as well as the office of town Marshal. Several members of the opposing faction were arrested on trumped-up charges, and some were killed with the faction in power falsely claiming they had resisted arrest. The conflict gained national attention and on two occasions the Governor sent troops to maintain order with little effect. Eventually a posse of as many as 100 individuals was organized and armed by Daniel Boone Logan with the tacit consent of Governor J. Proctor Knott and Governor-elect Simon Bolivar Buckner. In a dramatic two-hour gun battle that took place in the center of Morehead, several Tollivers, including Craig Tolliver were killed and the Tollivers' control of the county was broken. Two men were later held to trial for the murder of Craig Tolliver but were acquitted