During mobilisation in 1939, the fort was prepared as an infantry support point. It served as an outpost for the Grebbe Line (forward defence line of the Dutch Water Line). Seven casemates were built around the fort and trenches and foxholes were dug. At the outbreak of war, on 10 May 1940, the fort was soon surrounded. A day later, nothing was left but to surrender.

As the fort on the junction of rivers was an orientation point for aircraft, a German anti-aircraft gun (FLAK) was placed there. The German occupiers also housed soldiers and prisoners of war in the fort.

After liberation, residents of evacuated Pannerden returned to their largely flattened village. Lacking everything, many building materials (mainly wood and bricks) were taken from the fort for house construction. Afterwards, a lot of ammunition dumped there during the war was also found.

Today, Fort Pannerden is a museum with many activities for young and old.