Born in Helmond, North Brabant, Bouma started his career at amateur club SV Rood-Wit '62 before joining PSV on a youth contract in 1994.

The PSV head coach at the time, Aad de Mos handed him his professional debut against Willem II on 26 October 1994 which his team lost 2–1.

At PSV, he played as a left winger and as forward because of his quick pace and direct passing, teaming up with Arnold Bruggink and at times, with Ruud van Nistelrooy.

When Arthur Numan departed to Rangers at the end of the 1999–00 season, Bouma was moved to left-back where he had to compete with Danish international Jan Heintze.

With the 2002 FIFA World Cup qualifiers entering its crucial stages, Bouma was handed his international debut for the Netherlands national team against the Republic of Ireland on 2 September 2000.

This turn in form also attributed to Bouma reclaiming his place in the Netherlands national team, playing in the friendly against Russia in February 2007, the tour of Asia in June 2007 and the following UEFA Euro 2008 qualifying fixtures.

On 9 February 2008, Bouma – who was in the process of making his 76th appearance in claret and blue – netted his only goal for the club in the 48th minute of the match against Newcastle United.

[9] Bouma said his goodbyes to the Villa faithful during half-time of the home defeat to Blackburn in their final league game, later stating that he intended to address the fans but "just couldn't do it" after becoming too emotional.

On 24 February 2011, Bouma was handed the captain's armband for the final five minutes of the UEFA Europa League match against Lille that PSV went on to win 3–1 on the day and 5–3 on aggregate.

Bouma was also included in the Dutch squad for UEFA Euro 2008, and he made two appearances, coming on as a 78th-minute substitute against France and playing the full 90 minutes against Romania.