Shekara da shekaru, Imam Khumaini ya yi yana karantar fa fikihu, Usul, sufanci da akhlak a makarantun Hawza na Kum da suka hada da Makarantar Fa'iziyya, Masjid al-A'azam, Masjid Muhammadiye, Makarantar Hajj Mullah Sadik da kuma Masallacin Salmusi da dai sauransu. Har ila yau ya kuma karantar da fikihu da sauran ilmummukan Ahlulbaiti (a.s) a masallacin Shaikh al-Ansari (r.a) da ke Najaf na tsawon shekaru 14, inda a nan ne a karon farko ya bayyanar da ra'ayin gwamnatin Musulunci cikin silsilar darussan da yake bayarwa na Wilayatul Fakih.