During his time at Arsenal, he scored a last-minute goal in injury time during the final match of the 1988–89 season, which allowed the club to claim the First Division title over Liverpool. Later in his career, Thomas went on to play for Liverpool and scored a goal for them in the 1992 FA Cup Final. He also had spells at Benfica and Wimbledon before retiring in 2001, after a career that saw him win medals in all of English football's top three domestic football trophies. He was capped twice by England.
He was born in Lambeth, London. After growing up as a Spurs fan Thomas 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. He was loaned out to Portsmouth in early 1987, playing three times, before returning to Arsenal. 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. Arsenal lost 1-0, but would go on to win the League Cup after a comeback in the second leg.
Thomas soon became a regular in the Arsenal side, making his league debut on 14 February 1987 in a 1-1 draw with Sheffield Wednesday at Hillsborough. By the end of that campaign he had played 12 league games as Arsenal finished fourth and had a League Cup winners medal, coming on as a late substitute as Arsenal defeated Liverpool at Wembley. He played 37 times, mainly at right-back, in the 1987-88 season, and scored nine goals - excellent for a player who mainly featured in defence. With the arrival of right-back Lee Dixon late in the season, Thomas was moved forward into midfield for the 1988-89 season. He appeared in that game alongside his Arsenal midfield colleague Brian Marwood, who had joined them from Sheffield Wednesday eight months earlier.
The highlight of Thomas's Arsenal career came in the 1988-89 title decider, on 26 May 1989. 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. Liverpool had won the FA Cup, and thus had a chance of completing a historic second Double. Arsenal had been top of the First Division table for most of the season, but Liverpool had overtaken them a few games before the end. Coming into the match, Arsenal were on 73 points with 71 goals for and 36 against (a goal difference of +35), while Liverpool were 3 points ahead on 76 points with 65 goals for and 26 against (a difference of +39). That meant that Arsenal needed to win by at least two goals to take the title (with points and goal difference equal, the team who had scored the most goals would be awarded the title). Liverpool had not lost by two goals at Anfield for nearly four years. After a goalless first half, Alan Smith scored soon after the restart, heading in a free kick from Nigel Winterburn. But as full-time approached it looked as if Arsenal were not going to score the second goal they needed. However, in injury time, in Arsenal's last attack, Thomas surged forward from midfield, running onto a Smith flick-on, evaded a challenge by Steve Nicol, and chipped the advancing goalkeeper Bruce Grobbelaar to score Arsenal's second, and win the title, Arsenal's first in eighteen years. The match was later featured in detail in a film based on the Nick Hornby book Fever Pitch.
By this stage, Paul Merson had emerged as a fine right-winger for the Gunners, in a position previously occupied by David Rocastle, who was switched to central midfield. However, Thomas remained a regular player despite the fierce competition in midfield. Thomas enjoyed another two seasons at Arsenal, winning a second League title in 1990-91. In all, he played 206 matches, scoring 30 goals. However, he fell out with Arsenal manager George Graham in the autumn of 1991. As a result, he was sold to the side he had helped conquer in 1989, Liverpool, with their manager Graeme Souness paying the Gunners £1.5 million for Thomas's services on 16 December 1991, by which time he had 163 league games for them and scored 24 goals. Thomas was named the 37th greatest player in the history of Arsenal in an online poll on the Arsenal website in June 2008.
Thomas made his Liverpool debut two days after signing, on 18 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.
Thomas scored his first goal for the Reds on 18 January 1992 in league victory over Oldham Athletic at Boundary Park. His first season at the club culminated with an FA Cup victory at Wembley against Sunderland. After a goalless first 45, Thomas scored the opening goal of the final after 47 minutes with a spectacular shot from a Steve McManaman cross. A second goal from Ian Rush made the final score 2-0, earning Thomas his first medal for his new club. However, after that, injuries began to blight Thomas's time at Anfield. He became a squad player who was largely used as cover for the likes of Jamie Redknapp and John Barnes.
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.
An £800,000 bid from Coventry City was accepted in early December 1997, but the transfer never happened. On 2 February 1998, Thomas was allowed to go out on loan to Middlesbrough, and made his debut two days later on 4 February in a 3-0 league win over Tranmere Rovers at the Riverside Stadium. He played 10 times for the Boro before he returned to Anfield. 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. Thomas's impression on the Anfield faithful during his time at the club was confirmed when he was voted in at No. 83 in 100 Players Who Shook The Kop, a poll conducted by Liverpool FC's official website in 2006 with over 110,000 fans voting.
Portuguese side Benfica, then managed by former Liverpool boss Graeme Souness, took Thomas to the Estádio da Luz on 1 August 1998, but his stay in Lisbon was an unsuccessful one as he found himself banished to the reserves after Souness was replaced by Jupp Heynckes. After two years with Benfica, he returned to England on 29 July 2000 to join Wimbledon, but after a single season in which he played nine times he retired from playing on 31 May 2001.
He was called up to the England squad under manager Bobby Robson. His debut came on 16 November 1988, at the age of 21, in the 1-1 friendly draw against Saudi Arabia in Riyadh. He made his second and final England senior appearance just over a year later, on 13 December 1989 in a 2-1 friendly win over Yugoslavia.
After retiring from football, Thomas set up his own security service. He also plays for the Liverpool legends team as well. Thomas currently resides in the city of Liverpool.