Fatigue initiation and the propagation of microcracks in a cortical bone is an initial phase of damage development that may ultimately lead to the formation of macroscopic fractures and failure of the bone. In this work, a time-resolved high-resolution X-ray micro-computed tomography (CT) was performed to investigate the system of microcracks in a bone sample loaded by a simulated gait cycle. A low-cycle (1000 cycles) fatigue loading in compression with a 900 N peak amplitude and a 0.4 Hz frequency simulating the slow walk for the initialization of the internal damage of the bone was used. An in-house developed laboratory X-ray micro-CT imaging system coupled with a compact loading device were employed for the in situ uni-axial fatigue experiments reaching a μ2μm effective voxel size. To reach a comparable quality of the reconstructed 3D images with the SEM microscopy, projection-level corrections and focal spot drift correction were performed prior to the digital volume correlation and evaluation using differential tomography for the identification of the individual microcracks in the microstructure. The microcracks in the intact bone, the crack formation after loading, and the changes in the topology of the microcracks were identified on a volumetric basis in the microstructure of the bone.