[2][3] Upon his return to England, he studied modern history at St. Catherine's College, University of Oxford and obtained his doctorate there in 1981.

[3] Parts of his thesis became the basis for his first book, published as Rising of the Red Shawls (1985), about the Menalamba rebellion in colonial Madagascar.

[3] The same year, he was appointed Desmond Tutu Professor of Youth, Sport and Reconciliation at the Vrije Universiteit in Amsterdam, where he worked until his death.

[8] The book was unpopular with the ANC for its account of abuses in the exile camps, but many of Ellis's allegations were later confirmed in the final report of the Truth and Reconciliation Commission.

[8][14] Ellis's The Mask of Anarchy (2001), about the Liberian civil war, was shortlisted for the African Studies Association's Herskovits Award,[3] but caused a minor scandal in West Africa when newspapers reported on the book's claim that Liberian warlord Charles Taylor engaged in ritual cannibalism.

[5] Some commentators labelled the book racist;[4] and Taylor, then Liberian President, sued Ellis in a London court, but later withdrew the charges.