In 1882, while teaching at Sumner, Clifford established the Pioneer Press, the state's first black newspaper. He advocated for the rights of African Americans locally and nationally. Clifford even criticized the all-white management of Storer College. The Pioneer Press remained one of the most respected black newspapers in the nation until it was closed by the federal government in 1917, due to Clifford's editorial criticisms of the United States' involvement in World War I. At the time of its demise, the Pioneer Press was the longest running black newspaper in the country.
Some of Clifford's most important contributions to black history were in the field of law. He studied with a white lawyer in Martinsburg, J. Nelson Wysner, and in 1887 became the first African American to pass the West Virginia bar examination. He argued two landmark cases before the West Virginia Supreme Court of Appeals.
In 1896, Clifford brought the first legal challenge of the state's segregated school system to the court. Thomas Martin, a black parent in Morgan County, wanted his children to have the opportunity to attend a local white school. Since the Martins were the only African-American family in the area, there was no separate school for the children. In the case of Martin v. Board of Education, the Supreme Court ruled the Martin children were not allowed to attend the white school even though the alternative meant not receiving an education. The Martin decision upheld the state's segregation policy, which was not overturned until the Brown v. Board of Education of Topeka, Kansas decision by the U.S. Supreme Court in 1954.
In 1898, Clifford was more successful in the case of Williams v. Board of Education of Tucker County. The Tucker County Board of Education had reduced the school term of African-American schools from eight to five months to save money. A black teacher, Carrie Williams, consulted Clifford for advice. He suggested she continue teaching for the entire eight months, despite the fact she would not be paid. When the board refused to pay Williams for the additional three months, Clifford took the case to court. The West Virginia Supreme Court found in favor of Williams, the first ruling in U.S. history to determine that racial discrimination was illegal.
In the area of civil rights, Clifford worked with his friend, W. E. B. Du Bois, to found the Niagara Movement in 1905. The Niagara Movement developed to counter Booker T. Washington's philosophy of working within the existing system to achieve gradual civil rights advancement. For his conservative ideas, Washington had become popular with white politicians of the time and had been invited to the White House by President Theodore Roosevelt. Unlike Washington's followers, participants in the Niagara Movement wanted immediate change. Clifford arranged the organization's second annual meeting in August 1906, held on the grounds of Storer College in Harpers Ferry. Participants walked barefoot to John Brown's Fort in a morning vigil honoring Brown's attempt to evoke a slave uprising in 1859. Clifford broke with the Niagara Movement when it formed the National Association for the Advancement of Colored People (NAACP) in 1909. Among other disagreements, he objected to the use of the word "colored" in the organization's title.
Clifford died in Martinsburg in 1933, at the age of eighty-five and was buried in the city's Mount Hope Cemetery. In 1954, his body was reinterred in Arlington National Cemetery in recognition of his service during the Civil War.
Researchers may wish to view the Clifford Family Collection (Ms2004-104), which includes photocopies of an early history of his family and an image of John Robert Clifford.