Although FRM II's thermal power is limited to 20MW, a maximum unperturbed thermal neutron flux of approx. 8x10¹⁴cm^-2s^-1 is obtained. FRM II thus displays the best ratio anywhere in the world of thermal neutron flux density outside the core to thermal power. The design of FRM II results, among other things, in extremely favourable background conditions, the basis for this being the particularly compact reactor core, consisting of only one fuel element and cooled with light water H₂0, which is arranged centrally in a large moderator tank. This moderator tank is filled with heavy water D₂0. The moderator tank is a diameter of approx. 2,5m and is as high as broad. The whole installation is inside the reactor pool (internal diameter approx. 5m). Owing to the low absorption levels of the latter, in comparison with light water, and the high level of leakage of fast neutrons from the compact core, a pronounced maximum of thermal neutron flux density builds up outside the core. This maximum is located approx. 12cm from the core surface, which makes it very readily accessible for experimental use. The secondary neutron sources (spectrum converters) and cold and hot sources are also to be found in this area.

The compact core consists of a single, cylindrical fuel element. Its inner diameter is 118mm, its outer diameter 243mm and its height is approx. 700mm. The fuel element with its packaging is approx. 1,3m high. Inside the fuel element there is the central control rod. Its one element of the active safety concept. The control rod controls nuclear fission and it's lifted during operation to compensate nuclear burn-up.

The fuel element is made up of 113 involuted, curved fuel plates. The fuel plates are produced by using the so-called picture frame technique. They consist of three layers. The fuel U₃Si₂ composed of a mixture of uranium silicide and aluminium powder is embedded in an aluminium matrix. Each fuel plate consists of a fuel zone - the so-called meat - sandwiched between cladding layers of aluminium. The general design of the cylindrical fuel element is comparable to most other high-flux reactors - the fuel plates of involute shape are arranged in a circle to provide cooling channels of constant width of 2,2mm. The core diameter of about 24cm is exceptionally small, leading to a very high unperturbed thermal peak flux (8x10¹⁴cm^-2s^-1) in the moderator, given a fairly small reactor power of 20MW. With a cycle length of about 50 days, 5 fuel elements will be required per year.

One single control rod in the central hole of the fuel element is used to control the reactor power. This rod is divided into an absorbing front section and a reflecting end section, in order to achieve a higher burn-up of the fuel. In order to homogenise the power and fission density, the uranium content in the outer zone of each fuel plate is reduced from 3gcm^-3 to 1,5gcm^-3. Furthermore a Boron ring is employed at the lower end of the fuel element to level the power density in this region.