Farrell was again top-scorer in 1896–97 as his 13 goals from 20 appearances (ever-present) helped the Saints claim the Southern League title for the first time, going the whole league season without defeat. By now team captain, Farrell received the Championship shield from Dr. Russell Bencraft, who was both president of the League and of the club, at a ceremony in the Artillery Drill Hall in Southampton. In the FA Cup, the Saints reached the Second Round Proper where they were defeated 3–1 at Newton Heath in a replay. Farrell played in all seven cup matches, scoring seven goals, including a hat-trick in an 8–2 victory over Swindon Town at the County Ground on 2 January 1897.