Now a day's non-conventional energy sources like PV power and Wind power sources are well developed because conventional energy sources are reduced day by day and at the same time the population has been increased. These drawbacks can be overcome by developing the microgrids. In current trends, microgrid protection is a very challenging task. Due to the interconnection of several distributed generators, fault currents are produced. Resistive type superconducting fault current limiter is used for the protection of microgrids because its operating time is very less, it stops the abnormal currents with in the first cycle and continuity of supply is possible. But R-SFCL had some disadvantages, it is not compensated for the reactive power. Then voltage levels are not compensated, for that reason series active power filters are used along with R-SFCL. Here series active power filters are compensating the voltage magnitudes and reduce the harmonics and then transient stability is improved in the microgrids. This work is done using MATLAB/Simulink.