In 2006, Johan Coetzee represented South Africa at the Under-18 Africa Cup. However, he switched allegiances to his country of birth, Namibia and made his test debut for them on 6 June 2015 in their 2015 Africa Cup match against Tunisia in Nabeul. He was also named in a 50-man Namibian training squad prior to the 2015 Rugby World Cup.
Coetzee then returned to South Africa to re-join the Free State Cheetahs for the 2015 Currie Cup Premier Division, despite expectations that he would miss the majority of the tournament through his involvement with Namibia at the 2015 Rugby World Cup.He was awarded SuperRugby player of the year in 2017.
Coetzee's name is one of the first to be written down when a team gets selected, and he is part of the Namibia Nation side at the 2019 Rugby World Cup in Japan.