During the Prague uprising against German occupation in 1945, the station was captured by the Waffen-SS on 8 May and 53 surrendered resistance fighters and non-combatants were massacred.

[2] Nowadays the station only serves regional and suburban trains, because the larger Praha hlavní nádraží does not have enough capacity.

In 2012, the reconstruction of the Masaryk Railway Station building began, led by the company Penta, which had purchased the surrounding land.

The "Masaryčka Connects" project is a significant urban regeneration effort in the centre of Prague, transforming the city's first railway station, into a modern transport hub.

In 2015–2016, Zaha Hadid supervised the conceptual design of a new mixed-use building that replaced a formal cargo terminal.The construction took place in 2020–2023, as some delay was caused by negotiations with heritage protection authorities.