The supercapacitor is becoming increasingly popular as an alternative energy storage technology for some of its extraordinary features. Precise state of charge (SOC) estimation is necessary for the effective and efficient operation of supercapacitors. Kalman filter based estimators are widely used for SOC estimation. The fractional order extended Kalman filter is used in this study to estimate the state of charge of supercapacitor. A 5F Maxwell supercapacitor has been used for this analysis. An integer order equivalent circuit model (ECM) has been considered and the parameter identification has been performed by GA-PSO (Genetic algorithm—Particle swarm optimization) algorithm. The performance of the filter has been compared with integer order extended kalman filter. The obtained result has been analyzed through the experimental data in terms of computational time and root mean squared error.