It was constructed and established, when Reverend William Pettigrew baptized and converted twelve Tangkhul Naga to Christian faith in 1901.
Baptized at Ngayira Rakhong (Ngayira Spring Pond), the first converts include, Hollei Rumthao, Sangmayang Kashung, Ramkaiphang Samrar, Leishisan Shaiza, Maninglum Kashung, Mangaleng Shaiza, Sakhayang Awungashi Shimray, Shangam Kasar, Kaphungkui Chiphang, Haora Mahongnao, Mashokring Kasomhung, and Thiksha Shokchui Kapai.
According to Shaiza, these include "maintenance of mohawk hairstyle (Hao Kuiret), brewing and drinking rice beer (Khor), attending traditional educational schools (Longshim), and participating in the death ritual ceremony (Kathi Kasham)",[2] making the Tangkhuls to forego these customs and culture.
The Western Missionaries disallowing such customs and traditions made Phungyo Baptist Church to grow along the lines of Western-Christian norms.
The CE later took the initiative of organizing a Church Choir, marking the birth with celebration at Pakahao Samrar's place (Alungtang Colony), on the second Sunday of March, 1953.