Kobayashi Station was opened on April 1, 1901 as a station on the Narita Railway Company for both freight and passenger operations. On September 1, 1920, the Narita Railway was nationalised, becoming part of the Japanese Government Railway (JGR). After World War II, the JGR became the Japan National Railways (JNR). Scheduled freight operations were suspended from November 1, 1961. The station was absorbed into the JR East network upon the privatization of the Japan National Railways (JNR) on April 1, 1987.