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.
Shortly after ascending the throne, he became engaged to Susanna Margarete of Anhalt-Dessau, a sister of Sibylle Christine.
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.