Christianity is the predominant religion of Mokokchung, with more than 95% of the population being Baptist. The Aos were the first of the Nagaland peoples to embrace Christianity in the 19th century, and the area is the hub of India's Baptist belt. The revivalist movement that swept the entire state of Nagaland in the 1970s originated in Mokokchung District and Mokokchung was a major centre. Impur, 15 kilometres away, is the centre of the Ao Baptist Arogo Mungdang (Ao Baptist Churches Convention). The main town Baptist church, located at the heart of the town, is one of the largest churches in Asia.
The other religions and faiths practiced in Mokokchung - mainly by immigrant business community from mainland India - are Hinduism, Sikhism and Islam