Nikola was born in Niš, SFR Yugoslavia, to a Croatian father and Serbian mother. Nikola's father Branko Karabatić, who was also a professional handball player, is originally from Vrsine, a village between Trogir and Marina in Croatia.[2][3][4] In his career, Branko played for the Železničar handball team from Niš, which is where he met his wife Radmila, who is originally from Aleksinac, Serbia.[5] The family moved to France after Nikola's father got a coaching job there when Nikola was 3 and a half years old. Nikola has a younger brother, Luka (born 19 April 1988).[3]
On 30 September 2012, he was involved in a match-fixing and arrested with his wife and his brother Luka.
In addition to French, he also speaks English, German, Spanish and Serbian.[6]