Nicolas Hénin was born to the family of a professor of Lycée Henri-IV and of academic Pierre-Yves Hénin; his grandfather was agronomist Stéphane Hénin. After graduating from lycée Henri-IV, he went on to study in a classe préparatoire at lycée Fénelon and graduated with a Licence in Geography and a Master in History from Panthéon-Sorbonne University. After studying Arabic, he specialised on the Middle East, and obtained a Master in International Relations with a thesis titled "Egyptian interarabic relations and the separate peace with Israel: November 1977" (), written during a research semester at Cairo at CEDEJ (). He then published articles in "Jeune Afrique" on the Sudan Civil War in 1997, and a photographic reportage on Yemen, , published in the monthly in November 1999.