This paper studies the performance of the distance relays for transmission lines equipped with hexagonal phase shifting transformers (PSTs). PSTs can effectively control the power flow in the transmission lines. However, they alter the operation of the distance protection elements. The influence becomes significant when the fault occurs through a resistance. In this paper, the combined effect of the PST and the fault resistance on the operation of the ground and phase distance relays is considered. The analysis accounts for the effect of the PST not only on near distance relays but also on relays protecting an adjacent line. System analysis is carried out and a compensation technique is derived based on the location of the fault concerning the installation location of the PST. An operation logic is proposed to coordinate the operation of different proposed compensated protection elements. This operation logic helps to select the proper method ensuring the reliability of the protection system. The proposed protection scheme uses the voltage and/or current measurements at the relay point in addition to the transferred PST tap position. Therefore, synchronized voltage and current measurements from different locations are not required. The simulation study conducted with MATLAB/Simulink shows the success of the proposed ground and phase distance elements to account for the combined effect of the PST and the fault resistance.