Webster County was created on January 10, 1860, from parts of Braxton, Nicholas, and Randolph counties. Named for Daniel Webster, the county occupies 556.2 square miles and is drained by the Elk, Gauley, Williams, Cranberry, Holly, and Little Kanawha rivers. The county seat is Webster Springs.

The earliest white settler was most likely Adam Stroud, who settled about 1769 near present Camden-on-Gauley on a tributary of the Gauley River now known as Strouds Creek. Three years later Stroud's family was destroyed by Indians. At about the same time, a Carpenter family sought refuge on Camp Creek from an Indian raid in what is now neighboring Braxton County. Solomon Carpenter, probably the first white child born in Webster County, was born on Camp Creek under a shelf-like cliff during this episode, an event commemorated in the traditional West Virginia fiddle tune, "Shelvin' Rock." Due to the remoteness of the area, the scarcity of tillable land, the ruggedness of terrain ranging in elevation from 1,000 feet to almost 4,000 feet, and the fear of Indians, few settlers followed until the end of the 18th century.

Since Webster County was created just before the outbreak of the Civil War, organization of the county government did not occur for several years. During this time, there was no government in the county and no taxes were collected. This lack of regular government gave birth to the so-called "Independent State of Webster," which had its own "governor" by the name of George Sawyer. In 1865, at the end of the Civil War, the formal organizing of Webster County took place, and county and district officials were elected. The population in 1860 was 1,555.

In the 1890s, a branch of the Baltimore & Ohio Railroad was built to the town of Cowen from Flatwoods, Braxton County. In the early 1900s, the West Virginia Midland Railroad Company built a narrow-gauge line to Webster Springs. Within a few years rails were laid through much of the county, serving the mines and sawmills. The first two decades of the 20th century were boom years for Webster County. Tourists came on the railroad to partake of the waters of the salt sulfur springs, and the coal and timber industries produced a vibrant economy. The Webster Springs Hotel was built in 1896 and enlarged in 1904. More than 11,000 people lived in Webster County by 1920.

The county had vast resources of timber and 19 seams of coal. The main employer for the timber and coal was the Pardee & Curtin Lumber Company. By the beginning of the 1940s, the timber industry was in decline, but coal mining boomed during World War II. Commercial mining had started in 1917, with an output of approximately 100,000 tons by 1929 and more than two million tons at the end of World War II. In 2009, over 4.5 million tons of coal was produced in Webster County. Surface mines accounted for 3.5 million tons.

The remoteness and ruggedness that had limited settlement also resulted in the preservation of areas of great scenic beauty with majestic hills and clear flowing streams. A large portion of the county is in the Monongahela National Forest. During the Roosevelt administration, several thousand acres of land near Hacker Valley was purchased by the federal Resettlement Administration, later transferred to the state, and is now Holly River State Park. In the 1920s along the Gauley River, the county established Camp Caesar, a 4-H camp which has become an important summer destination for religious, social, and institutional groups.

There were no public schools when Webster County was created in 1860. In September 1910, the first high school was opened in Webster Springs. Later, a high school was built in Cowen. In the 1970s, these high schools were consolidated into a single high school near Upper Glade.

Webster County's population peaked at 18,080 in 1940. The years following World War II saw a decline of coal industry employment and a migration of Webster Countians to factory towns in Ohio and elsewhere. This decline continued until 1970, when the county's population dropped below 10,000. The population was an estimated 9,043 in 2012.

With the increased interest in outdoor recreation and the construction of dams at nearby Summersville and Sutton, Webster County has become a popular destination. Since 1960, Webster County has been the site of the Woodchopping Festival. It is also the site of the Point Mountain Reunion, formerly called the Hamrick, Gregory, and Riggleman Reunion, held in August of each year.

Prominent Webster Countians include Arden Cogar (1934— ), world champion woodchopper, and Eli C. "Rimfire" Hamrick (1868—1945), a renown guide and woodsman. Twin brothers Hubert (1909— 69) and Hobert Skidmore (1909—46) were noted authors, Hubert producing Hawks Nest, the classic West Virginia novel.