In 1896, the ground level Muiderpoort Station was built around the crossing with the Java Street; however it disappeared with the construction of the railway viaduct in the 1930s.The current station, designed by the architect Schelling, dates to 1939 and, being a 'fork' station, it is the only one of its kind still remaining in operation in the Netherlands. A 'fork' station was snugly placed under the 'armpit' of two converging tracks.
For his project, the architect made extensive use of glass and created a spacious central entrance, which is now occupied by the bike shop. From the central hall and the ticket counters, two pedestrian tunnels led to the platforms. In the late 1990s the station was renovated, the central hall and the tunnels were given to small businesses, and the platforms became directly accessible from the street. In the course of 2002, the Dutch Railways closed the last ticket counter and the only way nowadays is to buy a ticket at a vending machine or use a public transit card.
The former signal box, which became a municipal monument in 2003, is the highest part of the station complex and is occasionally used for light art performances. The north facade of the building features the stained-glass window by the artist Heinrich Campendonk installed originally in 1939. It depicts bird migration, a common allegory for travel.
During World War II, Muiderpoort Station played a central role in the deportation of 11,000 Jewish Amsterdammers. Here the Jews were assembled and waited in queues for hours before being transported to Westerbork, a transit camp on the Dutch-German border from which they would be further transported to the death camps. A memorial plaque, designed by the artist Steffen Maas is on the Oosterspoorplein square outside the station. Looking towards the tracks, there is a bench with an embossed poem by Victor E. van Vriesland. The monument was unveiled by the then city mayor Job Cohen on October 3rd, 2002, the 60th anniversary to date of the first transport that left to the camps from the Muiderpoort Station. Since 2012, both the monument and the station have become part of the Westerborkpad, a 336-kilometer long travel and reflection route that stretches all the way from Amsterdam to the former transit camp Westerbork.