Henner was born at Bernwiller (Alsace). He began his studies in art as a pupil of Michel-Martin Drolling and François-Édouard Picot. In 1848, he entered the École des Beaux Arts in Paris, and took the Prix de Rome with a painting of Adam and Eve finding the Body of Abel in 1858. In Rome, he was guided by Flandrin, and painted four pictures for the gallery at Colmar among other works.
He first exhibited Bather Asleep at the Salon in 1863 and subsequently contributed Chaste Susanna (1865), now in the Musée d'Orsay. Other noted works include: Byblis turned into a Spring (1867); The Magdalene (1878); Portrait of M. Hayem (1878); Christ Entombed (1879); Saint Jerome (1881); Herodias (1887); A Study (1891); Christ in His Shroud and a Portrait of Carolus-Duran (1896); a Portrait of Mlle Fouquier (1897); and The Dream (1900).
The Levite of the Tribe of Ephraim (1898) was awarded a first-class medal. Among other professional distinctions, Henner also took a Grand Prix for painting at the Paris Exposition Universelle of 1900. He was made Chevalier of the Legion of Honour in 1873, Officer in 1878, and Commander in 1889. In 1889, he succeeded Cabanel in the Institut de France.
Henner died at age 76 in Paris.
Henner had numerous pupils; among them the Romanian artist Dimitrie Serafim. From 1874 to 1889, organized with Carolus-Duran, what he called "the studio of the ladies" for women were not allowed entry to the École des Beaux-Arts. Some also served as his models. One of these was Dorothy Tennant who later married Henry Morton Stanley.
Suzanne Valadon (1865-1938) also worked as one of his models.
- E Bricon, Psychologie d'art (Paris, 1900); C Phillips, Art Journal (1888)
- Frederick Wedmore, Magazine of Art (1888).
- Isabelle de Lannoy, Catalogue raisonne Jean-Jacques Henner 1829-1905 
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