Niňaj made an unexpected international debut under Ján Kozák on 19 November 2013 in a memorable first UEFA-recognised match against Gibraltar (0–0), when he tactically replaced Jakub Sylvestr in the 85th minute.[3] However, he failed to make another appearance under Kozák until his resignation in October 2018.
After Niňaj joined Fortuna Sittard, where he experienced an incomparably more successful season to the previous ones, he was again nominated to the national team, initially as an alternate.[4] Niňaj's first nomination to the national team nomination after over 5 years happened on 28 May 2019 when coach Pavel Hapal called him up for a double fixture in June - a home friendly against Jordan, to which, unusually, 29 players were called-up and a UEFA Euro 2020 qualifying fixture against Azerbaijan, played away on 11 June 2019. The squad was to be reduced to 23 players for the latter fixture.[5]
