In July 2017, Mokoena received his first call-up to the senior national team by former SuperSport United manager Stuart Baxter, who had departed the club at the end of the 2016–17 domestic season, for the nation's 2018 African Nations Championship qualifiers. He made his debut on 15 July against Botswana and was praised following the match for his ability to "carry the team on his shoulders". The following year, he scored his first international goal in South Africa's 2019 Africa Cup of Nations qualification win over Seychelles. His goal also contributed towards the nation recording its largest ever victory with the match ending 6–0 in favour of South Africa.