This paper presents a power quality compensation of the autotransformer-fed railway system using Matlab/SimPowerSystem and especially investigates two installation methods of the shunt active power filter (SAPF) along the autotransformer-fed railway systems; one configuration describes the SAPF installed at the substation and the other is the SAPF at the sectioning post. Also, the novel SAPF control algorithms based on the synchronous reference frame are proposed. A comparative study on two SAPF configurations and the corresponding control algorithms is investigated comprehensively through the case study.