Mogi das Cruzes station was built and opened by North Railway on 6 November 1875.
Due to the growing of the city of Mogi das Cruzes, EFCB built a new building, opened on 16 September 1929, as the place was a terminus for commuter trains of the "Central".
In the 1950s, it was expanded again, being reopened on 15 March 1958. The current station was built by RFFSA on 20 August 1984. Since 1994, it is operated by CPTM.
References
^Mennucci Giesbrecht, Ralph. "Mogi das Cruzes" (in Portuguese). Estações Ferroviárias do Brasil. Retrieved 18 July 2019.
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indicates planned stations. 
indicates stations being constructed.