FRM II is optimised for beam tube applications. Almost 50% of experiments are performed using cold neutrons. The concept is based on the use of a compact core containing a single cylindrical fuel element installed in the centre of a moderator tank filled with heavy water. Cooling is performed with light water from the reactor pool. The reactor is controlled by means of the central control rod inside the fuel element. To shut it down, an additional, independent system of five shutdown rods is provided in the moderator tank. Each system is individually capable of shutting the reactor down quickly and permanently at anytime.

The compact construction of the fuel element means that more than 70% of the neutrons leave the uranium zone and build up to a maximum thermal neutron flux density (undisturbed 8x10¹⁴cm^-2s^-1) at a distance of 12cm from the surface of the fuel element. This region of maximum flux density can be utilised for experiments; here there is arranged, distributed around the circumference, a series of beam tube tips and various vertical irradiation channels. The experimental stations are then located outside the reactor pool in extensions of the beam tubes in the experimental hall and on neutron guides in the neutron guide hall. The neutron guide hall connects the FRM II building with the old reactor building, the "Atomic Egg". It offers an experimental area approximately equal to that of the experimental hall.

Die kompakte Bauweise des Brennelements führt dazu, daß mehr als 70% der Neutronen die Uranzone verlassen und in einem Abstand von 12cm von der Oberfläche des Brennelements das Maximum der thermischen Neutronenflußdichte (ungestört 8x10¹⁴cm^-2s^-1) aufbauen. Dieser Bereich größter Flußdichte ist für Experimente nutzbar. Hier werden, auf den Umfang verteilt, eine Reihe von Strahlrohrnasen und diverse vertikale Bestrahlungskanäle angeordnet.
Die eigentlichen Experimentierplätze befinden sich außerhalb des Reaktorbeckens in Verlängerung der Strahlrohre in der Experimentierhalle sowie an den Neutronenleitern in der Neutronenleiterhalle. Die Neutronenleiterhalle verbindet das FRM II-Gebäude mit dem alten Reaktorgebäude, dem Atom-Ei. Sie bietet etwa eine gleichgroße Experimentierfläche wie die Experimentierhalle.