As a youngster Sean played for Top of the Hill Celtic F.C. in the Derry and District League. As he got older he broke into the Derry City team in the position of striker and scored a hat trick on his debut. Hargan later converted to left back, where he offers total commitment to the side. This has endeared him to the fans. Hargan has scored more than 50 competitive goals for the Candystripes, including a decisive header away to IFK Gothenburg in the 2006 UEFA Cup qualifying round. Also during the 2006 league season, Derry City escaped punishment for fielding a banned Hargan due to the league failing informing Derry City in the correct timeframe. By the end of that season, Hargan had made a total of 393 appearances for the club - that makes him the club's third highest appearer ever. Hargan was described as a great servant for the club and is mostly remembered for the goal he scored in the Europa League against IFK Gothenburg which saw Derry to a 1–0 victory on the night. After Derry's City's European experience, Shelbourne were reported to have shown interest in the left back, but Hargan pledged his loyalty and stayed with the Candystripes until the end of the 2008 season.