During the Second World War there were an equal amount of German Soldiers as native residents on Schiermonnikoog, 60. As part of the Atlantic Wall these soldiers build a village of bunkers to defend themselves against the Allied forces. The codename for this village was Schlei, the German name for the fish species tench. Besides bunkers the village consisted of radar installations, anti-aircraft guns and camouflaged barracks. 200 construction workers from the mainland helped building this complex.

One of the bunkers which was build was of the type Seeburg. This bunker was a central post and was used as a communication centre. Here radio signals were collected to, amongst other things, be able to intercept Allied bombers. It is in this bunker that the Bunkermuseum Schlei is housed. Bunkermuseum Schlei is managed by Foundation Bunkermuseum Schlei. This foundation has as goal to collect, preserve and exhibit goods and knowledge of the Second World War. The foundation also provides guided tours and lectures.

Every few years the museum has a new exhibition on a specific subject concerning the Second World War on and around Schiermonnikoog. Examples of this are the narrow-gauge railway which was on Schiermonnikoog during the Second World War and an exhibition within the context of 75 years of liberation.