The integrality of the numbers $A_{n,m}={(2n)!(2m)!}/{n!m!(n+m)!}$ was observed by Catalan as early as 1874 and Gessel named $A_{n,m}$ the super Catalan numbers. The positivity of the q-super Catalan numbers (q-analogue of the super Catalan numbers) was investigated by Warnaar and Zudilin [‘A q-rious positivity’, Aequationes Math. 81 (2011), 177–183]. We prove the divisibility of sums of q-super Catalan numbers, which establishes a q-analogue of Apagodu’s congruence involving super Catalan numbers.