It was named for Thomas Jefferson, author of the Declaration of Independence and third President of the United States.

The county's courthouse was the site of the trial for the abolitionist John Brown after his October 1859 raid on the federal armory in Harpers Ferry.

Brown was sentenced to death for murder, treason against the Commonwealth of Virginia, and conspiring with slaves to rebel.

On December 2, 1859, John Brown was taken from the Charles Town jail a short distance to an open field and hanged.

The county was a frequent site of conflict during the Civil War, as Union and Confederate lines moved back and forth along the Shenandoah Valley.

However, many voters were absent in the Confederate Army when the vote was taken and they refused to accept the transfer upon their return.

[9] In 1863, West Virginia's counties were divided into civil townships, with the intention of encouraging local government.

This proved impractical in the heavily rural state, and in 1872 the townships were converted into magisterial districts.

[10] Jefferson County was initially divided into five townships, which became magisterial districts in 1872: Averill, Bolivar, Chapline, Grant, and Shepherd.

In February 2007, Jefferson County Sheriff's Department Corporal Ronald Fletcher was shot and critically wounded during a stand-off at the residence of the girlfriend of a suspect, Dorsey Cox.

Cox had been at his girlfriend's house retrieving personal items in violation of a court-ordered protective order.

He is alleged to have beaten Mark Daniel Haines, who later pleaded guilty to bank robbery, during his arrest on December 27, 2010.

Shirley and 14 other "John Doe" law enforcement officers were also the subject of a civil rights lawsuit filed by Haines.

Shirley pled guilty to federal civil rights charges of and was sentenced to a year in prison.

For much of the 20th century, the county trended strongly Democratic due to historical sympathies for Confederate Virginia.

Despite its strong support for Republican presidential candidates in recent years, local Democrats still have success in Jefferson County.