He studies social conflict and social movements, especially ethnopolitical conflict and the use of nonviolent methods. He has focused much of his work on Northern Ireland, addressing issues such as conflict transformation and the strategic "choreography" of parading disputes. Some of his publications have also addressed third-party nonviolent intervention and the role of nonviolent social movements in the fall of the Soviet Bloc. Lee is a former Chair of the Peace, War, and Social Conflict section of the American Sociological Association.