Raja won his first World Championships medal in 2006 in Eton, Great Britain, where ha was a member of the bronze-winning quadruple sculls team with Andrei Jämsä, Tõnu Endrekson and Igor Kuzmin.

At the 2008 European Rowing Championships in Marathon, Greece he won a gold medal in the quadruple sculls event with Jüri Jaanson, Tõnu Endrekson and Andrei Jämsä.

Allar Raja made his first appearance at the Olympics in Beijing 2008 competing in the quadruple sculls event with Igor Kuzmin, Vladimir Latin and Kaspar Taimsoo.

[2] Raja won his second World Championships bronze medal in Poznań in 2009, where he competed in the double sculls event with Kaspar Taimsoo.

For the 2011 European Championships Raja and Taimsoo formed a new quad scull team with Tõnu Endrekson and Andrei Jämsä.

In summer of 2013 Raja and Taimsoo formed a new quadruple scull crew with young prospects Sten-Erik Anderson and Kaur Kuslap.

At the 2013 European Championships, held in Seville, Spain Raja competed in the double sculls event with Kaspar Taimsoo.