This paper presents an optimized fractional order controlled cascaded synchronous buck-boost converter for a wave/ultra-capacitor (UC) hybrid energy system. Due to the irregular wave dynamics, the extracted energy from a wave energy converter (WEC) shows aperiodic voltage swells and sags. To eliminate the stochastic wave effects on the electrical side of the WEC, a power electronic interface scheme based on buck and boost converters named as cascaded synchronous buck-boost converter (CSBBC) is designed and a solar charged UC unit is integrated to the wave energy conversion system (WECS). The proposed CSBBC with UC stabilizes the DC-bus voltage and improves the energy utilization of WECS. The simulation and experimental results of the CSBBC and UC are investigated to show modeling success of these systems. In order to test the performance of the fractional order PID (FOPID) controller, a classical PID controller is also employed. The parameters of both controllers are tuned by flower pollination algorithm which utilizes an error-based fitness function. The results show that proposed power electronic system with UC unit works effectively to compensate irregular wave effects under different load and variable voltage tracking control cases. Also, it is emphasized that optimized FOPID controller provides higher performance than optimized PID controller in terms of transient and steady-state responses in control of both DC-bus and load voltages.