Dr. Anton Pannekoek (1873-1960), who had been appointed as lecturer of astronomy and mathematics in 1919, became the director. The Institute started as a research institute with the 1921 appointment of its first technical staff member, then 15-year old David Koelbloed (1906-1977). In 1925 Pannekoek was appointed Professor of Astronomy, remaining half-time lecturer of mathematics.

Pannekoek’s research was focused on the structure of the Milky Way and on stellar astrophysics. He was the founder of astrophysical research in the Netherlands. This field of research remained the focus in the Institute under his successors Prof. Herman Zanstra (1894-1972), who started in 1946, and Bruno van Albada (1911-1972), who succeeded Zanstra in 1959.

When Albada was succeeded in 1974 as director by Edward van den Heuvel (b.1940), the latter started research in high-energy astrophysics, focused on the evolution of massive stars and the formation and physics of neutron stars and black holes.

The present-day scientific staff consists of 16 astronomers that study a rich range of research topics, including exo-planets, the most massive stars and merging stars, supernovae, the interiors of neutron stars, and supermassive black holes. In 1982 it was decided to name the institute after Anton Pannekoek.

At first, the institute occupied a few rooms in the loft of the University’s Oude Manhuis Poort building in the center of Amsterdam. After the Second World War, it moved to a former primary school at the Roetersstraat, and in 1968 to the 9th through 11th floors of the then new mathematics building Roetersstraat 15 (now housing the Faculty of Psychology).

In 1991 the Institute moved to the NIKHEF building at Science Park. As of 2009, the institute is located at Science Park 904 in the Faculty of Science building.  The Anton Pannekoek Observatory is located right on top of the institute, on the roof of the faculty building, and can easily be recognized by its two landmark telescope domes.

In the academic year 2021-2022, the API celebrated it's 100th birthday with a scientific conference and a podcast, among other things. As part of the conference, Professor Ralph Wijers also gave a lecture about the life of Anton Pannekoek. The podcast and the lecture are in Dutch and can be enjoyed through the following links.