Swindon Town manager Steve McMahon signed Allison in 1995 for a fee set by tribunal of £475,000. A roaming player for the club, Allison's ability to hold the ball up whilst others advanced in support and also help in defence earned him inclusion in "Swindon Town Football Club 100 Greats". He left Swindon for Huddersfield Town, his home town team, for the highest transfer fee of his career, £800,000. However he moved again in September 1999 to Tranmere Rovers for £300,000. He was cup-tied for their run to the 2000 Football League Cup Final. During his three-year stay at Tranmere he netted 32 goals in 117 appearances.