The local spatial heterogeneity of the material properties of the cortical and trabecular bone extracted from the mouse tibia is not well-known. Nevertheless, its characterization is fundamental to be able to study comprehensively the effect of interventions and to generate computational models to predict the bone strength preclinically. The goal of this study was to evaluate the nanoindentation properties of bone tissue extracted from two different mouse strains across the tibia length and in different sectors. Left tibiae were collected from four female mice, two C57BL/6, and two Balb/C mice. Nanoindentations with maximum 6 mN load were performed on different microstructures, regions along the axis of the tibiae, and sectors (379 in total). Reduced modulus (Er) and hardness (H) were computed for each indentation. Trabecular bone of Balb/C mice was 21% stiffer than that of C57BL/6 mice (20.8 ± 4.1 GPa vs. 16.5 ± 7.1 GPa). Moreover, the proximal regions of the bones were 13–36% less stiff than the mid-shaft and distal regions of the same bones. No significant differences were found for the different sectors for Er and H for Balb/C mice. The bone in the medial sector was found to be 8–14% harder and stiffer than the bone in the anterior or posterior sectors for C57BL/6 mice. In conclusion, this study showed that the nanoindentation properties of the mouse tibia are heterogeneous across the tibia length and the trabecular bone properties are different between Balb/C and C57BL/6 mice. These results will help the research community to identify regions where to characterize the mechanical properties of the bone during preclinical optimisation of treatments for skeletal diseases.