Mokotjo captained South Africa's U12 national team to victory at the 2003 Danone Nations Cup in France and was named as the Player of the Tournament. He was a member of the South Africa U20 squad that competed at the 2009 U20 World Cup and he made one appearance at the tournament, playing the opening 66 minutes of the team's 2–1 defeat to Ghana in the round of 16. Mokotjo played for the U23 team during its unsuccessful attempt to qualify for the 2012 Summer Olympics.