Raman microspectroscopy is an elegant and efficient tool for chemical analysis of the samples since it provides information about the structure, conformation, and changes of molecules both in pharmaceutical formulation and in the biological tissue. It is especially useful for samples containing water since water absorption is not dominating the Raman spectrum, as it happens in the case of infrared spectroscopy. Analysis of several formulations for onychomycosis treatment is shown as the example of Raman microspectroscopy application in pharmaceutics. Differences between the formulations are shown to be linked to their efficiency in the infection treatment. Comparison of Raman microspectroscopy as the tool to analyze pharmaceutical formulations, their efficiency and stability is made in relation to the other spectroscopical and microscopical methods and the advantages and disadvantages of several techniques are discussed. The application of the results obtained in this study is demonstrated on further improvement of the formulation in development.