A novel sensitive high-throughput high-performance liquid chromatography assay is developed and validated for the simultaneous determination of everolimus and clobetasol propionate in pharmaceutical formulations. The chromatographic separation is achieved on a Zorbax Eclipse XDB-C18 reversed-phase column using a gradient elution, with solvent A: ammonium acetate (pH 6.8; 0.01 M) and solvent B: acetonitrile. The mean recovery ranges from 95.1% to 100.0% for clobetasol propionate and from 97.9% to 103.7% for everolimus. The limit of quantitation for each analyte is 0.02 microg/mL. The percent relative standard deviations are less than 3% for intra- and inter-day analyses. The proposed method can be used for the routine quality control of everolimus and clobetasol propionate in complex pharmaceutical formulations, especially the drug-delivery systems with a low total drug-load.