Argonne National Laboratory (ANL) of USA and Kharkov Institute of Physics and Technology (KIPT) of Ukraine have been collaborating on the conceptual design development of an experimental neutron source facility consisting of an electron accelerator driven sub-critical assembly. The neutron source driving the sub-critical assembly is generated from the interaction of 100KW electron beam with a natural uranium target. The sub-critical assembly surrounding the target is fueled with low enriched WWR-M2 type hexagonal fuel assemblies. The U-235 enrichment of the fuel material is <20%. The facility will be utilized for basic and applied research, producing medical isotopes, and training young specialists. With the 100KW electron beam power, the total thermal power of the facility is ∼360kW including the fission power of ∼260kW. The burnup of the fissile materials and the buildup of fission products continuously reduce the system reactivity during the operation, decrease the neutron flux level, and consequently impact the facility performance. To preserve the neutron flux level during the operation, the fuel assemblies should be added and shuffled for compensating the lost reactivity caused by burnup. Beryllium reflector could also be utilized to increase the fuel life time in the sub-critical core. This paper studies the fuel cycles and shuffling schemes of the fuel assemblies of the sub-critical assembly to preserve the system reactivity and the neutron flux level during the operation.