After starring for the South Africa Schools, under-19, and under-21 sides, and captaining at all three levels, Van Niekerk received the rare honour of being called up to the Springboks directly from the U21 side in 2001, in spite of never having played a game in either the Currie Cup or Super 12. He made his debut against the All Blacks in Cape Town.
Van Niekerk has experienced injury troubles throughout his senior-level career. When healthy, however, he is considered able to compete with virtually any back-row player in the world. He scored important tries for the Boks in home wins over the Wallabies in the 2002 Tri Nations Series and the 2004 Tri Nations Series. He has often been used as an "impact player" off the bench, especially in the 2005 Tri Nations Series.
In 2002, he was voted the South African "Player of the Year". In the first match of the 2008 Tri Nations Series against the All Blacks in Wellington, he was a surprise choice to start at No. 8. He was expected to play for the Northampton Saints however his contract was terminated before he arrived, reportedly because of constant injury problems. At the moment he plays for RC Toulon, a club in France.