Heinersdorf was first mentioned in a 1319 document when it was sold by Margrave Waldemar of Brandenburg to the Hospital of the Holy Ghost in Berlin.

In 1920 it was incorporated into Greater Berlin and belonged to the former Pankow borough, until it merged with Karow, Blankenburg and Weissensee in 1985.

Originally part of a planned town hall that was never built, it later served as a Flak tower and as a listening station of the Red Army.

Heinerdorf was often in the media during 2008 due to controversy around the establishment of the Khadija Mosque by the Ahmadiyya Muslim Community.

The federal highway (Bundesstraße) 109 running along the street Prenzlauer Promemade to the A114 Autobahnzubringer Prenzlau motorway marks Heinersdorf's western border.