For the first 90 years of West Virginia’s history as a state, public education and most businesses and other public accommodations were segregated. One of the first successful lawsuits in the nation challenging segregated schools was decided by the West Virginia State Supreme Court of Appeals in 1887. In Carrie Williams v. The Board of Education Fairfax District, attorney J. R. Clifford argued that "discrimination against people because of color alone as to privileges, immunities and equal protection of the law is unconstitutional." The Supreme Court found in Williams’ favor.

The second conference of the Niagara Movement, led by W.E.B. DuBois, met at Storer College in Harpers Ferry in 1906. It was a significant gathering in the history of civil rights in America. The Niagara Movement, which had first met in 1905 at Niagara Falls, New York, resulted in the founding of the National Association for the Advancement of Colored People (NAACP) in New York in 1910. The Harpers Ferry meeting commemorated the 1859 raid by John Brown and his band on the federal arsenal there for arms in an attempt to free the slaves.

West Virginia was spared the worst of the lynching era, which cost the lives of thousands of African Americans in the late 19th and early 20th centuries. President Woodrow Wilson finally spoke out against lynchings, but Congress never enacted anti-lynching legislation. In contrast, the West Virginia legislature enacted anti-lynching legislation in 1921. A decade later, a mob in Greenbrier County hanged two Black men, Tom Jackson and George Banks, on a telephone pole after a shootout left two White constables dead. Under the law, Greenbrier County was forced to pay $5,000 to each estate of the lynched victims. Governor Conley deplored the lynchings. "Such matters must not be tolerated in West Virginia," he said. Up to that time, the state had had a reported 35 lynchings. Jackson and Banks added two more to the sobering total.

The anti-lynching bill was co-sponsored by Delegate Harry Capehart, of McDowell County, a Black Republican from a region of the coalfields known as "the Free State of McDowell." The presence of Capehart and other African Americans in the legislature indicated that voting was never a major problem for West Virginia Black citizens, although they faced the other indignities and discriminations of the Jim Crow era. Segregation prevailed in schools, restaurants and hotels, places of entertainment, and other public facilities.

Another Black legislator, Delegate T. G. Nutter, a Kanawha County Republican, was an NAACP lawyer. He represented the Huntington African American couple Lewis and Cora White in a successful lawsuit against restrictive real estate covenants in the late 1920s. The couple sued H. B. White in the landmark case of White v. White. In this ruling, the West Virginia Supreme Court outlawed racial and religious discrimination in the sale of property.

In 1928, the high court desegregated the Charleston library in a lawsuit that Nutter represented for A. H. Brown, E. L. Powell, and W. W. Sanders. The city of Charleston had previously maintained a separate library for Black citizens. The court said that taxpayers' money could not be used for a main library and exclude Black taxpayers.

Willard L. Brown, the son of A. H. Brown, was the lead lawyer for the West Virginia NAACP in the historic U.S. Supreme Court school desegregation ruling in 1954. Generally known as Brown v. Board of Education, the far-reaching case included West Virginia and 16 other states, and the District of Columbia. West Virginian John W. Davis, the 1924 Democratic candidate for president and later a powerful New York lawyer, took the other side of the case, arguing in behalf of the state of South Carolina for the continuation of segregation. Governor Marland accepted the ensuing high court decision as the law of the land. West Virginia school integration proceeded with a minimum of disturbance although not as rapidly as supporters had hoped. By the end of the 1957 school year only 20 counties were considered fully desegregated with protests against integration in McDowell and Mercer counties.

The desegregation of public places was a different story. They became targets of protest demonstrations, mainly by the Congress of Racial Equality (CORE) and ad hoc student groups. In Huntington, Marshall University students organized the Civic Interest Progressives, with leaders Pat Austin and Phil Carter. Protest demonstrations focused on the White Pantry Restaurant among holdout establishments. On August 11, 1958, CORE targeted three Charleston eateries, with sit-ins at the Woolworth, Kresge, and Newberry five-and-ten-cent stores. Faced with a backlash of bad publicity and boycotts, the three stores soon changed their policies and began allowing African Americans to eat in their establishments. Charleston CORE leaders Elizabeth Gilmore and Cynthia Burks conducted sit-in demonstrations at the lunch counter of the Diamond, then the premier department store in the Kanawha Valley. In Bluefield, CORE members sat in at downtown places and picketed the YWCA-YMCA. They were organized by Othella Jefferson, a professor of education at Bluefield State College. Federal Judge Ben Moore ruled against racial discrimination at the Sky Chief Restaurant at Kanawha (now Yeager) Airport in 1955. A. H. Brown filed the lawsuit against Sky Chief, through his son, Willard Brown. Charleston's downtown lunch counters would not seat Blacks until 1958. And even by 1962 the West Virginia Human Rights Commission reported that "many places continue to refuse service and some follow different policies at different times."

Most public places had opened their doors to all by the time Congress passed the 1964 Civil Rights Act. In that year, Howard W. McKinney, executive director of the West Virginia Human Rights Commission, reported that all major hotels were desegregated, except the Shenandoah Hotel in Martinsburg, which accepted African Americans for lodging rooms but not in the dining area. The West Virginian Hotel in Bluefield opened its doors to Blacks after a sit-in in the spring of 1964.

Senator Robert C. Byrd opposed the Civil Rights Act, filibustering unsuccessfully to prevent its passage. Byrd later expressed regret over his opposition.

Following the passage of the Civil Rights Act, 40 percent of West Virginia Black students still attended all-Black schools. In the seven counties with the most Black residents, seven out of 10 Black students still attended all-Black schools. The clause "white and colored persons shall not be taught in the same school" would remain in West Virginia's Constitution until 1994, and even then, 42 percent of West Virginia voters and 16 counties voted to keep it in.

However, two years after the passage of the Civil Rights Act the state Human Rights Commission reported "a general response of compliance with the Civil Rights Bill" though there was "concern during the summer months directed at swimming pools." Rock Lake Pool in South Charleston was the site of bitter protests over its segregation policy in the summer of 1965.

In the 21st century, unfinished civil rights work remains in education and civil justice, said West Virginia NAACP President James Tolbert at the 2002 State Capitol observance of the Martin Luther King Jr. holiday. In 2014, West Virginia Human Rights Commission director Marykaye Jacquet said the commission still gets complaints about racism, mostly in employment.