The station lay directly on the border between the administrative districts of Wedding and Prenzlauer Berg, established in 1920, during the Weimar Republic. In 1945, at the beginning of the post-World War II occupation of Germany, Wedding was assigned to the French sector, Prenzlauer Berg to the Soviet. The closing of the intra-city border on August 13, 1961, separated the area of the train station from Schwedter Straße, which was the actual sector border, and from the slope along the elevated Friedrich Ludwig Jahn Sportpark. South of the former station building, the border zigzagged around the (then blocked off) Eberswalder/Oderberger/Schwedter/Bernauer Str. crossing, deviating to the west and continuing on the southern side of Bernauer Straße, where the Berlin Wall Memorial stands today. At that intersection, in West Berlin territory, stood one of the famous observation decks that allowed a look over the Wall into East Berlin.
Due to the difference in height between the sports park and the former station area, the East German border guards faced a difficult situation for more than 20 years: the border strip sat on an inclined plane, on the steep slope in front of Jahn Stadium, while the level train station area belonged to West Berlin. Through a territory exchange in 1988, East Berlin acquired the eastern part of the railway station premises, thus extending about one kilometer of the border 50 meters to the west. Approximately 300 meters of the rear wall still stand there today.