In the 2004–05 season, Vlaar made his unexpected Eredivisie debut at the age of 20. Due to suspensions within the first team squad at the end of the season, Vlaar was paired up with the experienced centre back Barry Opdam on 23 April 2005 in the away match against RKC Waalwijk (2–1). Five days later, on 28 April 2005, Vlaar made his European debut. The youngster was part of the starting line-up in the UEFA Cup semi final away match against Sporting Clube de Portugal (2–1). Vlaar played three Eredivisie matches and two UEFA Cup matches in his debut season.
While Vlaar thought the season 2005–06 would be his breakthrough year, AZ coach Louis van Gaal kept choosing for more experienced players. Vlaar was part of the starting line-up thrice, while he came in as a substitute in four matches, having a total of seven Eredivisie appearances in his first half-year. Despite Vlaar's substitute status at AZ, the youngster impressed the Netherlands coach Marco van Basten enough to invite him for his first international matches. As Vlaar was only playing at AZ for a youth contract, various sides were interested to offer Vlaar more playing time. AZ were keen to offer Vlaar a new and improved contract, however Vlaar had no interest in staying at AZ as he felt blackmailed by AZ coach Louis van Gaal: "He told me I would only play at emergencies if I wouldn't sign the new contract". The young centre back was close to a deal with Ajax and was spotted in London, as he was visiting Martin Jol's Tottenham Hotspur with his father and agent. However, on 28 December 2005, Vlaar signed a three-and-a half-year deal with Feyenoord.
Vlaar represented the Netherlands at various youth levels. However, he had most success with the Netherlands U20 on the 2005 FIFA World Youth Championship and with Netherlands U21 on the UEFA European Under-21 Football Championship in 2006 and 2007
The 2005 FIFA World Youth Championship took place in the Netherlands between 10 June and 2 July 2005. Vlaar, reserve captain behind Hedwiges Maduro, was an important player in the Dutch team and was active in every match the team played on the tournament. Netherlands U20 had a smooth run through the group stage, winning their three matches respectively easy against Japan U20 (2–1), Australia U20 (3–0) and Benin U20 (1–0). After beating Chile U20 (3–0) in the next round, the Netherlands U20 reached the quarter finals against later finalist Nigeria U20 (1–1 aet 9–10 pso). Despite Vlaar's equalizing goal and successful penalty kick, the Netherlands U20 didn't advance to the next stage.
In the few matches the promising defender played, he made enough of an impression to be noticed by Marco van Basten, the coach of the Netherlands national team. He was selected for the qualifier against Romania in June 2005, but did not play. The first international match in which he played was a match against the Czech Republic on 8 October 2005.