The NIC is headed by a Board of Directors. A Scientific Council advises the Board of Directors and the Contract Partners on issues related to the R&D fields of the Research Groups, the continued enhancement of computer equipment and other resources for NIC. The Peer Review Board reviews and evaluates the submitted research proposals and makes recommendations for appropriate grants of supercomputer resources. The Scientific Council, the Peer Review Board, and the Board of Directors are supported by a Scientific Secretariat.

At Research Centre Jülich (FZJ) the supercomputers and the required IT infrastructure are operated by the Jülich Supercomputing Centre (JSC). Jülich will host a new research group.

DESY at Zeuthen operates the APE special-purpose computers and hosts the Research Group "Elementary Particle Physics"

GSI provides computer resources in Darmstadt. A Research Group "Nuclear and Hadron Physics" is in preparation.