A simple empirical method that extracts the elastic moduli of both thin films and the underlying substrates is proposed and validated by both new nanoindentation experiments and published data. Deconvolution of thin film’s elastic properties from the substrate is achieved by statistical estimation, where a simple function relating the elastic moduli of the thin film and substrate to the film-substrate composite modulus is used to fit the experimental data plotted against the logarithmic indentation depth normalized by film thickness. Experimental data from a wide range of soft and hard films on substrate were used to demonstrate the deconvolution and validate the method. The estimated elastic moduli of thin films and substrates agree well with their corresponding standard values or values obtained by other methods. The advantages of this method are discussed, and recommendations are made on how to design experiments to obtain reliable data for this method.