Construction of the Prague-Bubny railway station began in 1866 out of the need to connect the Prague-Dejvice station to what is now Masaryk Railway Station via the Negrelli Viaduct. The station was operational just two years later, and between 1869 and 1873, it was surrounded by additional technical buildings (a large depot, including a paint shop, a sawmill, and extensive workshops). Many of these ancillary structures remained in use until 2013. Following unsuccessful attempts to have them designated as historic landmarks, the buildings—with the exception of the station building and the waterworks building—were demolished in the fall of 2015. The station itself ceased operations in 2022.

In 1941, a gathering point was established in the nearby Radiotrh building of the Prague Sample Fairs (on the site of today’s Mama Shelter hotel) for Jewish residents who had received summonses to board transports. The location was chosen precisely because of its proximity to the station. The first transport departed from the Prague-Bubny station on 16 October 1941, bound for the Łódź ghetto. This was followed by 70 transports, through which nearly fifty thousand Czechoslovak Jews and individuals designated as Jews under the Nuremberg Laws were deported to the ghettos in Łódź and Terezín. The last transport departed in January 1945.

In March 2015, thanks to an initiative by the nonprofit organization Shoah Memorial Prague, the art installation “The Gate of No Return” by sculptor Aleš Veselý was unveiled next to the station building; it has become a monumental symbol commemorating the dark history of this place. The Shoah Memorial sought to transform the train station into a place of remembrance that would commemorate historical events. In 2017, an architectural design by ARN Studio from Hradec Králové won the competition.

In 2021, the Czech Ministry of Culture established the subsidized organization “Memorial of Silence” with the aim of carrying out the reconstruction of the train station building. At the turn of 2024 and 2025, the organization was renamed the Bubny Center for Memory and Dialogue, and reconstruction began in the summer of 2025. The mission of this subsidized organization is to preserve the memory of the victims of the Holocaust and to create a living space that connects the past with the present through educational and cultural programs.