Johnson joined the political science faculty at the Massachusetts Institute of Technology in 1964. In 1969 he was promoted from Assistant Professor to Associate Professor. From 1968 to 1970, Johnson took a leave to serve as executive director of the Roxbury, Bostoncommunity development corporation The Circle Inc. He also held visiting positions at Harvard Business School, Boston University, and The Fletcher School of Law and Diplomacy. In 1970, Johnson published the book The Cameroon Federation: Political Integration in a Fragmentary Society, the basis of which was his PhD dissertation. The Cameroon Federation was reviewed as being one of the very first published accounts of the political system of Cameroon that was more than a brief historical treatment. This system was of particular interest because Cameroon was an officially bilingual nation with both French and British colonial histories, and the country had recently voted to unify after 40 years of administrative and cultural division. Johnson argued that Cameroon's success in forging one coherent state could serve as a case study that generalized to inter-African relations, since the continent too had the potential for sharp divisions between regions with French colonial history and regions with British colonial history. In a review of The Cameroon Federation, Claude E. Welch summarized the resulting political situation as "one of the oddest federations on the contemporary political map", which "exhibits all the usual splinterings of tropical African states". In The Cameroon Federation Johnson studied the extent to which the different parts of Cameroon had become truly politically integrated, and not just superficially joined, concluding that the development of substantial state capacity in a unified Cameroon was not certain. During the 1960s and 1970s, Johnson was a member of the Africa Policy Task Force for the George McGovern 1972 presidential campaign and the Foreign Affairs Study Group of the Democratic Party Advisory Council, as well as UNESCO's U.S. National Committee. He was also a founder of the Boston Pan-African Forum. During the 1980s, Johnson was involved in local activism to promote divestment from South Africa. As president of the TransAfrica Boston Support Group in 1982, he has been credited with playing an important role in the passage of divestment legislation by the Massachusetts House of Representatives, overriding a veto by Governor Edward J. King. For the remainder of his academic career Johnson continued to study institutional development and international relations, with a particular focus on Africa.