Strontium (Sr²⁺) ions are an effective therapeutic agent for the healing of osteoporotic bone fractures and are therefore used, for example, in form of strontium-modified bone cements. In order to reduce animal testing in further implant materials development in the future, a simulation of the Sr²⁺ release and transport in bone would be helpful. For such a simulation, knowledge of the experimental parameters for Sr²⁺ mobility in different compartments of bone (mineralised bone, bone marrow) is essential. In a previous study, we developed an experimental protocol for transport studies in bovine bone marrow by time-of-flight secondary ion mass spectrometry (ToF-SIMS). In the current proof-of-concept study, we investigated Sr²⁺ diffusion for the first time in bone marrow of rat bone sections. Additionally, orbitrap secondary ion mass spectrometry (OrbiSIMS) was applied for unambiguous signal identification of lipids and fatty acid species in rat bone marrow. Detailed 2D and 3D mass spectrometric imaging analyses, depth profiling as well as OrbiSIMS spectrometric analysis revealed faster Sr²⁺ diffusion in rat bone marrow areas with low intensity of lipid and fatty acid signals than in areas with higher lipid/fatty acid content. These results could be confirmed by histological staining and additional analysis of Sr²⁺ diffusion into pure fat sections.