In 1819, Fairmont was founded as Middletown, Virginia. It was named Middletown because either it was in the middle of two cities, Morgantown and Clarksburg, or Fleming's first wife, Elizabeth Hutchinson, was originally from Middletown, Delaware. That same year, a road was built between those two cities.

Fleming's new town was about halfway between the two cities, which made it a resting point. The town was incorporated as Middletown on January 19, 1820.The current borders of Marion County were established in 1842, and Middletown was named the county's seat. At that time, William Haymond Jr. suggested that the town's name be changed to Fairmont because the town had a beautiful overlook of the Monongahela River, giving it a "fair mount".

The Borough of Fairmont was incorporated in 1843 by the Virginia General Assembly.In 1863, during the American Civil War, Confederate General William E. Jones and his men raided Fairmont and cut the Union's supply lines to take food and horses. They also burned the books from the personal library of Governor Francis Harrison Pierpont.Many of the first buildings in Fairmont were poorly constructed.

By 1852—little more than 30 years after the city's founding—a large portion of Fairmont was reported to be run-down and dilapidated. Reports from 1873 indicate that these buildings had continued to fall into disrepair. On April 2, 1876, a fire destroyed a large portion of the city's business district, as well as many houses in the area.

The continuing dilapidation of the city's buildings may have contributed to the fire; the large number of coal mines under Fairmont may have also played a role.Between 1891 and 1901—in a span of only 10 years—Fairmont's population had increased from 1,000 to 7,000. The City of Fairmont was chartered in 1899; as a result of the charter, the city absorbed the surrounding towns of Palatine (also known as East Side) and West Fairmont.

By 1901, Fairmont was an important commercial center. Many railroads—including the Baltimore and Ohio Railroad on its way from Cumberland, Maryland to Wheeling—traveled through the city. By this time, Fairmont was also the leading center of the coal trade industry in northern West Virginia, employing some 10,000 workers in the coal mines around Fairmont.By 1978, an issue with Fairmont's land experiencing subsidence appeared because the remains of Fairmont's 19th-century coal mines were crumbling.

As a result, over the following years, the federal government along with other institutions spent money to fix the subsidence issue to prevent damage to the town.