From 1950 to 1966, Johnson was a history instructor and professor at LeMoyne College, and East Carolina College. He was also an archivist at Fisk University. Later, Johnson was recruited by the American Missionary Association to organize in archival fashion the large collection of documents housed by the American Missionary Association at Fisk University. Johnson was a logical choice for this role since his doctoral dissertation had been on the history of the American Missionary Association. He was for two years on leave of absence from Fisk University for this task. Their collection numbered some 300,000 items at the time, and Johnson further extended their collection in addition to preserving it. By 1963 the collection was sufficiently well organized that Johnson opened it for public use. In 1966, the United Church Board of Homeland Ministries, part of the American Missionary Association, created the Race Relations Department, with Johnson as director. Initially the Race Relations Department provided the financial support for the Amistad Research Center. He continued his work on what would be the Amistad Research Center under the auspices of the Race Relations Department. In 1969, the Amistad Research Center became an independent entity, and it relocated to Dillard University in New Orleans, Louisiana, the following year. Johnson remained director, and he succeeded in continuing to build the collection and the finances of the Amistad Research Center. Johnson served as director of the Amistad Research Center until 1992, at which time he acquired emeritus status, continuing to publish scholarly articles on African-American History. He additionally served as interim director from May 1995 to May 1996 as the Amistad Research Center recruited a new director. Johnson was a consultant for the Steven Spielberg movie Amistad. In a publication describing the significance of the Amistad Research Center, Johnson stated:
Selected publications
Johnson's scholarly articles pertained to abolitionism, African-American history and archives administration.
Clifton H. Johnson, , Yale News, January 25, 2002.
Johnson was married to Rosemary Johnson with whom he had sons Charles Johnson and Robert Johnson and daughter Virginia Johnson. He resided in Eastern New Orleans for the majority of his tenure as director of the Amistad Research Center. He died at his home in Eugene, Oregon, on May 21, 2008.