This paper presents and analyses protection schemes for a series active compensator, which consists of a Unified Power Quality Conditioner (UPQC) or a hybrid active power filter. The proposed series active compensator operates as a high impedance "k(D)" for the fundamental components of the power frequency during over current conditions in the distribution system. Two control strategies are proposed in this paper. The first strategy detects the fundamental source current using the p-q theory. The second strategy detects the fundamental component of the load current in the Synchronous Reference Frame (SRF). When over currents occur in the power distribution system momentarily, the proposed schemes protect the series active compensator without the need for additional protection circuits, and achieves excellent transient response. The validity of the proposed protection schemes is investigated through simulation and compared with experimental results using a hybrid active power filter systems.