Transformers are essential components of electric power transmission systems. The reliability of the transformer protection system is crucial to ensuring the continuity of the electric power supply. Inrush current occurs when there is a significant change in voltage on a particular side of the transformer winding, such as when the transformer is switched on. This phenomenon is not a fault, but it can generate enormous currents and, in some cases, cause differential and Restricted Earth Fault (REF) protection to initiate an unnecessary circuit breaker trip. This paper presents a case study of the analysis of transformers protection system setting at PT PLN (Persero) UPT Durikosambi to mitigate the inrush current phenomenon. This paper will analyze the characteristics and behavior of the inrush current phenomenon based on recorded data when an inrush occurs from a protective relay. Furthermore, the implementation of second harmonic blocks in differential and REF transformer protection is discussed. The results showed that this logic function could mitigate the inrush current phenomenon, thereby preventing unnecessary trips and improving the reliability of the differential and REF protection.