From 1986 to 2000, Khalaji trained in the seminaries of Qom, the traditional center of Iran's clerical establishment. There he studied theology and jurisprudence, earning a doctorate and thoroughly researched on modern intellectual and philosophical-political developments in Iran and the wider Islamic and Western worlds. In Qom, and later in Tehran, Khalaji launched a career in journalism, first serving on the editorial board of a theological journal, "Naqd va Nazar", and then the daily "Entekhab". In addition to his own writing, he has translated the works of the Islamic humanist scholar Muhammad Arkoun and other modernist Muslim intellectuals.