Since he made his first appearance for the national team in 2012, Mabkhout has been an instrumental member of the United Arab Emirates, being part of the side during the 2015 and 2019 AFC Asian Cup, as well as participating in FIFA World Cup qualification and regional tournaments like the Arabian Gulf Cup. On 31 August 2019, in a friendly game against minnows Sri Lanka, Mabkhout opened the scoring with his 50th international goal, and would go on to get a hat-trick in an eventual 5–1 win. This made Mabkhout only the second Emirati player in history to score 50 goals for the side after Adnan Al Talyani. On 10 October 2019, Mabkhout scored a hat-trick against Indonesia in a 5–0 win, to become UAE's all-time leading goalscorer.