Farrell returned to Southampton, now playing at The Dell, in May 1899 to replace Abe Hartley who had moved on to Woolwich Arsenal. Both he and the club started the League season well with twelve wins from the first fifteen games, in which Farrell scored eleven goals, until an injury in February put Farrell out for several weeks, allowing Roddy McLeod to stake a claim for the centre-forward position. Although Farrell returned to the side in mid-March after a run of three league defeats, he was unable to find the form of the early part of the season and was in and out of the side, scoring only once from his last six appearances. Southampton finished the season in a disappointing third place having lost five of their last seven games.