Charles Henri was the third child and only surviving son of the second marriage of Charles IV, Duke of Lorraine (there had been no children from his first marriage). This second marriage, contracted while Duke Charles was in exile, was not canonically recognized because the separation between the duke and his first wife, Nicole de Lorraine, was not recognized as a valid annulment by the Holy See. Charles Henri's claim to inherit Lorraine was therefore disputed, and rule of the duchy had been obtained by his father's younger brother through French intervention. He was born in Brussels.

On 27 April 1669, in Bar-le-Duc, he married a cousin, Anne Elisabeth de Lorraine, daughter of Charles de Lorraine, Duke of Elbeuf of the House of Guise. The princess was known as Mademoiselle d'Elbeuf, a style derived from her father's title. They had one son, Charles Thomas de Lorraine (1670–1704), who later took his father's non-territorial title, Prince of Vaudémont. This son was killed in battle near Ostiglia.

In exile like his father, Charles Henri served in the Spanish-Habsburg army against France, fighting in numerous battles. In 1675, he was made a knight of the Order of the Golden Fleece. He served in the Nine Years' War in Flanders under William III of England.

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