This paper proposes a novel application of micro-superconducting magnetic energy storage (μSMES) for a rooftop photovoltaic (RPV) system to mitigate its output power intermittency. Low cost magnesium di-boride (MgB2) superconductor wire is used for the SMES system. To compensate the power fluctuation of RPV systems flexible charging and discharging strategies are considered. The proposed control strategy will help to mitigate the effects of high photovoltaic (PV) penetration on the distribution grid. In addition, the state of charge (SoC) of the MgB2-based μSMES has been taken into account to prevent the over-charging and over-discharging. The performance of a 10 kW RPV-SMES is evaluated using the PSIM environment. The simulation results show that the SMES system can compensate for the RPV output fluctuation with the SoC limitation.