After growing up as a Tottenham Hotspur fan,[4] he signed for rivals Arsenal as a schoolboy in 1982, turning professional on 31 December 1984 at the age of 17, just months after leaving school.

His Gunners career started with a baptism of fire, as Thomas made his debut in the first leg of a League Cup semi-final against Tottenham Hotspur at Highbury on 8 February 1987.

Thomas soon became a regular in the Arsenal side, making his league debut in place of the suspended Viv Anderson on 14 February 1987 in a 1–1 draw with Sheffield Wednesday at Hillsborough.

Steve Williams February suspension was the perfect opportunity for Thomas to be shifted into central midfield in order to add more energy and dynamism to this area.

[8] The First Division match between Liverpool and Arsenal at Anfield had been postponed due to the Hillsborough Disaster, and as a result was moved to the very end of the season, after the FA Cup final.

He was in the England squad, and among the substitutes, when Brazil came to Wembley 28 March 1990, but the injury wrecked his chances of going to the World Cup Finals.

During the championship run-in Thomas appeared in the Daily Mirror, under the headline "My Highbury Hell", criticising Arsenal manager George Graham.

The Football Association took stern action and fined Thomas £3,000, and his relationship with Graham was beyond repair, reflected in a 1-0 loss in his final Arsenal match against West Ham United 2 November 1991 at Highbury.

[16] As a result, he was sold to Liverpool, with their manager Graeme Souness paying the Gunners £1.5 million for Thomas's services on 13 December 1991.

In a repeat of his Arsenal debut, his first match for Liverpool was against Tottenham Hotspur (though this time at White Hart Lane), coming on as a substitute for Jan Mølby in the 56th minute of a 2–1 victory.

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 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.

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.

By this time manager Roy Evans was fielding Øyvind Leonhardsen and Danny Murphy ahead of Thomas, which led to him being surplus to requirements at Anfield.

His debut came on 16 November 1988, at the age of 21, in the 1–1 friendly draw against Saudi Arabia in Riyadh, thus becoming the first player in Arsenal's history to play at five different levels for his country.