This paper discusses the robust stability and stabilization of polynomial fractional differential (PFD) systems with a Caputo derivative using the sum of squares. In addition, it presents a novel method of stability and stabilization for PFD systems. It demonstrates the feasibility of designing problems that cannot be represented in LMIs (linear matrix inequalities). First, sufficient conditions of stability are expressed for the PFD equation system. Based on the results, the fractional differential system is Mittag–Leffler stable when there is a polynomial function to satisfy the inequality conditions. These functions are obtained from the sum of the square (SOS) approach. The result presents a valuable method to select the Lyapunov function for the stability of PFD systems. Then, robust Mittag–Leffler stability conditions were able to demonstrate better convergence performance compared to asymptotic stabilization and a robust controller design for a PFD equation system with unknown system parameters, and design performance based on a polynomial state feedback controller for PFD-controlled systems. Finally, simulation results indicate the effectiveness of the proposed theorems.