In the development of topical drugs intended for local effects in the skin, one of the major challenges is to achieve drug penetration through the external barrier of the skin, stratum corneum, and secure exposure to the viable skin layers. Mass spectrometric imaging offers an opportunity to study drug penetration in a variety of skin models by mapping the spatial distribution in different skin layers after topical application of the drug. In this study, we used time-of-flight secondary ion mass spectrometry (TOF-SIMS) and scanning electron microscopy (SEM) to image the distribution of three drug molecules in skin tissue cross sections of inflamed mouse ear. The three compounds, roflumilast, tofacitinib, and ruxolitinib, were topically administered to the mouse ears, which were subsequently cryosectioned and thawed for the analyses. The results reveal that the combination of TOF-SIMS and SEM was beneficial for interpretation of drug distribution. SEM identified the different skin layers, while spatial distributions of all three compounds could be visualized by TOF-SIMS, showing that the drug was primarily distributed into, or on the top of, the stratum corneum. Imaging of endogenous skin components like cholesterol, phospholipids, ceramides, and free fatty acids showed distributions in good agreement with the literature. One limitation of the TOF-SIMS method is sensitivity, typically allowing for analysis in the millimolar range rather than the pharmacologically relevant micromolar range. However, the data presented demonstrate the potential of the technique for studying the penetration of drugs with different physicochemical properties in skin.