Niranam Church has a rich history of being the symbol of Christian faith in Kerala and a citadel of Orthodox Christianity since its inception in AD 54 by St Thomas, one of the twelve apostles of Jesus Christ. St Thomas reached Kerala in AD 52 and started preaching the gospel. He founded 8 churches, which are called 'Ezhara Pallikal', meaning seven and half churches. These were at Kodungallur, Kollam, Niranam, Nilackal (Chayal), Kokkamangalam, Kottakkayal (Paravoor), Palayoor (Chattukulangara) and Thiruvithamkode (the half church). St. Thomas who had great respect for the Holy Virgin, named all these churches after St. Mary. At Niranam, St. Thomas baptised many people and ordained people with social eminence as priests, to administer the church.
The church founded by St Thomas at Niranam was adjacent to Sri Thrikpaleswara Hindu Temple of Lord Shiva. Some adversaries of the new faith later took out the cross, founded by the Apostle and threw it into the neighboring river. When St Thomas returned to Niranam after two years (AD 54) he heard about this and went in search of the cross. He found it at a place in the down stream and again founded the church at that place, which is believed to be the present location of the church. According to the available records, the present building is the fourth, which was built in 1912. The third building was built in 1259.