Van der Vaart came through the ranks at Ajax with national teammates John Heitinga and Wesley Sneijder.
Initially, he signed for Ajax on a trial basis as a ten-year-old, but was eventually enrolled permanently after impressing the coaches.
At the age of 17, Van der Vaart made his debut for the Ajax senior side in a 1–1 draw with FC Den Bosch on 19 April 2000 in the 1999–00 season.
After he broke into the Ajax first team, Van der Vaart was "hailed as the new Johan Cruyff".

In the 2000–01 season, Ajax manager Co Adriaanse increased Van der Vaart's playing time by moving him to the attacking midfielder position.
He was voted European Talent of the Year by Italian football website CalcioManager.

The next season, Van der Vaart suffered a serious knee injury and was out for several months.
Shortly after returning to action, he re-injured the same knee on 2 April 2002, requiring an operation that involved the removal of his entire meniscus This injury forced him to miss the run-in to Ajax’s successful Eredivisie campaign and their Dutch Cup triumph against Utrecht in the 2001–02 season, but it did not stop him being named the Netherlands' Talent of the Year.

In 2002–03, Ajax won the Amsterdam Tournament, though injury limited Van der Vaart to 21 league appearances, in which he scored 18 goals.
After his return to fitness, he scored a vital goal in the UEFA Champions League away to Lyon, which propelled Ajax into the knockout stages.

In the first half of 2003–04, his performances were poor.
Van der Vaart admitted he was overweight, and the media criticized his celebrity lifestyle with his then-fiancée, The Music Factory VJ Sylvie Meis.
He became an influential figure once again as Ajax claimed another league title.
By that stage, Van der Vaart had firmly established himself as one of the stars of the Ajax team, as well as one of the most popular players in the Netherlands.

Van der Vaart was named team captain by coach Ronald Koeman for the 2004–05 season.
During an international match against Sweden on 18 August 2004, he was injured by then-Ajax teammate Zlatan Ibrahimović, which led to the sale of Ibrahimović to Juventus two weeks later, following controversial accusations that the Swede had intentionally tried to hurt Van der Vaart.
As a result, Van der Vaart took Ibrahimović's spot as striker.
He was unhappy at being played out of position, and following his refusal to play on the wing in a Champions League match in December, he was stripped of the team captaincy by Koeman.

In September, a league match against ADO Den Haag was temporarily halted by the officials due to incessant chants by opposing fans directed at Meis.
The incident, coupled with his ongoing injury problems that resulted in an average of only 23 league appearances in five seasons with Ajax, led him to announce that he was leaving the club at the end of the year.
Van der Vaart came through the ranks at Ajax with national teammates John Heitinga and Wesley Sneijder. Initially, he signed for Ajax on a trial basis as a ten-year-old, but was eventually enrolled permanently after impressing the coaches. At the age of 17, Van der Vaart made his debut for the Ajax senior side in a 1–1 draw with FC Den Bosch on 19 April 2000 in the 1999–00 season. After he broke into the Ajax first team, Van der Vaart was "hailed as the new Johan Cruyff".
In the 2000–01 season, Ajax manager Co Adriaanse increased Van der Vaart's playing time by moving him to the attacking midfielder position. He was voted European Talent of the Year by Italian football website CalcioManager.
The next season, Van der Vaart suffered a serious knee injury and was out for several months. Shortly after returning to action, he re-injured the same knee on 2 April 2002, requiring an operation that involved the removal of his entire meniscus This injury forced him to miss the run-in to Ajax’s successful Eredivisie campaign and their Dutch Cup triumph against Utrecht in the 2001–02 season, but it did not stop him being named the Netherlands' Talent of the Year.
In 2002–03, Ajax won the Amsterdam Tournament, though injury limited Van der Vaart to 21 league appearances, in which he scored 18 goals. After his return to fitness, he scored a vital goal in the UEFA Champions League away to Lyon, which propelled Ajax into the knockout stages.
In the first half of 2003–04, his performances were poor. Van der Vaart admitted he was overweight, and the media criticized his celebrity lifestyle with his then-fiancée, The Music Factory VJ Sylvie Meis. He became an influential figure once again as Ajax claimed another league title. By that stage, Van der Vaart had firmly established himself as one of the stars of the Ajax team, as well as one of the most popular players in the Netherlands.
Van der Vaart was named team captain by coach Ronald Koeman for the 2004–05 season. During an international match against Sweden on 18 August 2004, he was injured by then-Ajax teammate Zlatan Ibrahimović, which led to the sale of Ibrahimović to Juventus two weeks later, following controversial accusations that the Swede had intentionally tried to hurt Van der Vaart. As a result, Van der Vaart took Ibrahimović's spot as striker. He was unhappy at being played out of position, and following his refusal to play on the wing in a Champions League match in December, he was stripped of the team captaincy by Koeman.
In September, a league match against ADO Den Haag was temporarily halted by the officials due to incessant chants by opposing fans directed at Meis. The incident, coupled with his ongoing injury problems that resulted in an average of only 23 league appearances in five seasons with Ajax, led him to announce that he was leaving the club at the end of the year.
Rafael van der Vaart