The first footprints of Japanese Christians in New York date back to the 1890s, when the 1890 U.S. Census showed 2,039 Japanese on the U.S. mainland.
Almost 130 years ago, a man named Kinya Okajima walked from Oregon to New York State, where he met Toyohiko Takami, a future contributor to the Japanese American community, and laid the foundation for Japanese Christianity in New York.

Several Japanese churches and organizations arose from Manhattan Borough, but they were integrated into this Japanese American Church. By the time the Second World War began in 1940, there were three Japanese churches in New York City. At that time, discrimination against Japanese of Japanese descent and permanent resident holders intensified in the U.S., and Japanese on the West Coast were interned in camps, with as many as 4,000 Japanese being held at Ellis Island. Despite these harsh conditions, Japanese pastors visited the Japanese at Ellis Island and assisted the permanent residents by providing employment, funds, and counseling.

After the war, when the West Coast internment camps were abolished, many Japanese immigrated to New York City, and the size of the Japanese Christian community grew accordingly.