In this research, we discuss the construction of analytic solution of homogenous initial boundary value problem including PDEs of fractional order. Since homogenous initial boundary value problem involves Caputo fractional order derivative, it has classical initial and boundary conditions. By means of separation of variables method and the inner product defined on 𝐿 2 [0, 𝑙], the solution is constructed in the form of a Fourier series with respect to the eigenfunctions of a corresponding Sturm-Liouville eigenvalue problem including fractional derivative in Caputo sense used in this study. We defined a new inner product with a weighted function to get coefficients in the Fourier series. Illustrative example presents the applicability and influence of separation of variables method on fractional mathematical problems.