In this study, iterative reproducing kernel method (RKM) will be applied in order to observe the effect of the method on numerical solutions of fractional order Boussinesq equation. Hilbert spaces and their kernel functions, linear operators and base functions which are necessary to obtain the reproducing kernel function are clearly explained. Iterative solution is constituted in a serial form by using reproducing kernel function. Then convergence of RKM solution is shown with lemma and theorem. Two problems, “good” Boussinesq and generalized Boussinesq equations, are examined by using RKM for different fractional values. Results are presented with tables and graphics.