After completing her education, Toft joined the faculty at Harvard University where she was a professor of international politics at the Kennedy School of Government and Assistant Director of the John M. Olin Institute for Strategic Studies.
When the Olin Institute closed in 2007, Toft then established and directed the Initiative on Religion in International Affairs at the Kennedy School.
During this period, she also spent four months as Professor of Strategy at the Naval War College in Newport, Rhode Island.
Toft is a member of the Council on Foreign Relations, the Minorities at Risk Advisory Board, and the Political Instability Task Force.
Her work has been recognised through numerous awards, grants and fellowships, including being named Carnegie Scholar by the Carnegie Foundation of New York for her research on religion and violence in 2008, awarded a Fulbright Scholarship to Norway in 2012, and granted Princeton's World Politics Fellowship in 2015 .