 In the 1996–97 season, with Graeme Souness as manager, Neilson made a total of 29 appearances as "The Saints" struggled near the foot of the table, missing relegation by one point, having been in last place with five matches to play.Despite Saints' poor form, Neilson earned one further international cap while he was with the club, in a 7–1 defeat by Netherlands on 9 November 1996.Souness left the club in the summer of 1997, being replaced by Dave Jones who brought in several new players, including left-back Lee Todd from his previous club, Stockport County.