In 1951, Henry was a founding member of the Regional Council of Negro Leadership (RCNL). The main instigator and head of the organization was Dr. T.R.M. Howard, a prominent black surgeon, fraternal organization leader, and entrepreneur in the all-black town of Mound Bayou, Mississippi.
The RCNL promoted a program of civil rights, voting rights, self-help, and business ownership. Instead of starting from the “grass roots," it sought to “reach the masses through their chosen leaders” by harnessing the talents of blacks with a proven record in business, the professions, education, and the church. Henry headed the RCNL's committee on "separate but equal" which zeroed in on the need to guarantee the "equal."
Other key members of the RCNL included Amzie Moore, an NAACP activist and gas station owner from Cleveland, Mississippi and Medgar Evers, who sold insurance for Dr. Howard in Mound Bayou. Henry aided the RCNL's boycott of service stations that failed to provide restrooms for blacks. As part of this campaign, the RCNL distributed an estimated twenty thousand bumper stickers with the slogan “Don’t Buy Gas Where You Can’t Use the Rest Room." Beginning in 1953, it directly challenged separate but equal and demanded integration of schools.
Henry was a participant in the RCNL’s annual meetings in Mound Bayou between 1952 and 1955. These often attracted crowds of over ten thousand.
Frequently a target of racist violence, Herry was arrested in Clarksdale repeatedly and in one famous incident was chained to the rear of a city garbage truck and led through the streets of Clarksdale to jail.
While Henry remained active in the RCNL until its demise in the early 1960s, he also joined the Mississippi branch of the NAACP in 1954 eventually becoming state president in 1959. He started the Mississippi Freedom Democratic Party (MFDP) and the Council of Federated Organizations (COFO). In 1961 he organized a boycott of stores in the Clarksdale, Mississippi area that discriminated against African Americans both as customers and employees. He chaired delegations of Loyalist Democrats to the 1968 and 1972 Democratic National Conventions. He was elected to the Mississippi House of Representatives in 1982, holding the seat until 1996.