The station was built around 1881 as Moriches station after the original Moriches station was renamed for the geographically correct Eastport, New York. At some point the station was renamed as well for the more geographically correct Center Moriches, New York. When East Moriches and Eastport Stations were closed by the LIRR on October 6, 1958, commuters who used those stations were advised to use Center Moriches station. This was the last railroad station in the Moricheses. The station house was razed in 1964, but continued as a platform. Although a new shelter was built sometime around 1985, it was finally closed on March 16, 1998. This station and a handful of others at the time were closed due to low usage.