John Robert ("J.R.") Clifford was born in 1848 in the small town of Williamsport, in what was then Hardy County, Virginia, near present-day Moorefield, West Virginia. Clifford's parents and grandparents were "free blacks" and had lived in that region of Virginia for several generations. There were no schools for colored children in the area. Clifford's parents sent him to Chicago to attend school, sometime in the early 1860s.

In 1864, at the age of fifteen during the American Civil War Clifford enlisted in the United States Colored Troops, and served with the 13th Regiment Heavy Artillery until 1865.

After the Civil War, Clifford learned the barber trade, and then operated a writing school in Ohio and West Virginia. In the early 1870s he enrolled in Harper’s Ferry newly formed Storer College , created to educate the region's African-American population. After earning his degree in 1877, Clifford became a teacher at, and then the principal of, a segregated public school for African Americans in Martinsburg, West Virginia.

In 1882, Clifford began to publish "The Pioneer Press", a newspaper that was distributed nationally to a largely African American audience. He published the newspaper until 1917; it was the longest running weekly newspaper dedicated to African American issues during that time period.

In 1887, Clifford became the first African American attorney admitted to the West Virginia State Bar. He practiced law for forty-five years and was active in both state and national politics. Clifford was the President of the National Independent League and the first Vice-President of the American Negro Academy. Clifford was among the founders of the Niagara Movement, with other prominent African-American civil rights leaders such as W.E.B. DuBois. 

In 1906, the Niagara Movement's first American meeting occurred in Harper’s Ferry, West Virginia. The Niagara Movement led to the formation of the NAACP a few years later and is considered to be the cornerstone of the modern civil rights movement.

In 1898, Clifford won a landmark CIVIL RIGHTS and education case before the West Virginia Supreme Court of Appeals. In Williams v. Board of Education, Clifford argued against the Tucker County Board of Education's decision to shorten the school year for African-American school children from nine months to five months, keeping a full term for white students. Mrs. Carrie Williams, the colored school's teacher, approached Clifford. He encouraged her to continue teaching for the full nine months, regardless of funding. Clifford then filed a lawsuit against the school board for Williams' back pay. Clifford won the case at a jury trial, and then won again before the WV Supreme Court of Appeals. The Court's decision bolstered equal educational rights for African American students statewide.

Clifford's victory in the Williams case occurred over fifty years before the landmark "Brown v. Board of Education case and was one of the few civil rights victories in a southern state's high court before the turn of the century. The J. R. Clifford Project, an organization dedicated to preserving Clifford’s legacy and researching his life, presents re-enactments of this trial.

In 1933, Clifford died at the age of 85 in Martinsburg, West Virginia. His remains are buried at Arlington National Cemetery.

Clifford was one of the founding members of the "Niagara Movement", which was organized and led by W.E.B. DuBois. The Niagara Movement called for full civil rights for black Americans and an end to legalized segregation, and is recognized as the cornerstone of the 20th Century civil rights movement and the forerunner to the NAACP. Clifford helped organize the first American Niagara meeting in 1906 at his alma mater Storer College in Harpers Ferry, West Virginia. In 2006, the Niagara Movement's Centennial was celebrated by the National Park Service at Harpers Ferry. The J. R. Clifford Project performed the "J.R. Clifford and the Carrie Williams Case" re-enactment program at the event.