Mampilly's research focuses on the nature of contemporary conflict processes, with an emphasis on Africa and South Asia. Based on fieldwork within insurgent-controlled territories in D.R. Congo, Sri Lanka and Sudan, he examines rebel behavior focusing on the governance of civilian populations. He is currently working on a book on popular protests in Africa with Adam Branch, and is the author of Rebel Rulers: Insurgent Governance and Civilian Life during War (Cornell University Press).