Nikolai Gubenko was born in the Odessa Catacombs during the Defence of Odessa, the youngest of five children. His mother was Russian and his father – a native Ukrainian; both of them died in 1942 during the Great Patriotic War. His father joined the Soviet Air Forces before Nikolai was born and was killed in action near Voroshilovgrad. His mother, a chief designer at one of the local plants, was interrogated during the Nazi-Romanian occupation of Odessa and killed after she refused to collaborate; her body was returned to Nikolai's grandfather "with traces of hanging".