Biwajima Station was opened on April 1, 1886 as Kiyosu Station(清洲駅,Kiyosu-eki) on the Japanese Government Railway (JGR) Tōkaidō Line. The station was relocated to its present location and renamed to its present name on April 16, 1906. The JGR became the JNR after World War II. The station building was rebuilt in March 1953. Along with the division and privatization of JNR on April 1, 1987, the station came under the control and operation of the Central Japan Railway Company. All freight services came to an end in 2006. A new station building was completed in December 2008.