Johann Ernst was the son of Count Albrecht of Hanau-Münzenberg-Schwarzenfels and his wife, Countess Ehrengard of Isenburg-Büdingen.
Johann Ernst was educated at the school of the former convent in Schlüchtern, which is now called the Ulrich-von-Hutten-Gymnasium, and the University of Basel.
The Thirty Years' War forced him and his family to Worms and later to Strasbourg, where they faced great financial difficulties.
The attending physicians, including Peter de Spina III, had only recognized the disease very late and had treated him with laxatives and bloodletting when he was dying.
Johann Ernst was succeeded by Friedrich Casimir, who was also Count of Hanau-Lichtenberg, thereby reuniting Hanau in a single hand, after a 184-year split.