The 1994–95 season saw Thomas claim his only other winner's medal during his time at Anfield, when the Reds won the League Cup final against Bolton Wanderers. Thomas was an unused substitute on the bench during that game, which saw McManaman scoring both the team's goals as Liverpool won 2–1. Thomas then helped Liverpool reach the 1996 FA Cup final, where he saw five minutes of action after coming on as an 85th-minute substitute for Rob Jones. He couldn't help the Reds prevent a 1–0 defeat at the hands of Manchester United. 1996–97 was a disappointing campaign for a Liverpool side who finished fourth in the Premier League after leading it during the winter, but Thomas re-emerged as a first team regular following the absence of Jamie Redknapp due to injury problems. However, when Redknapp was fully fit for the 1997–98 season, Thomas found himself on the sidelines again.