Meissonier began preparing for "1806, Jena" in 1887, in anticipation of the 1889 Exposition Universelle in Paris, though elements found in the painting are visible in studies and sculptures from as early as 1880. When the Exposition opened, "1806, Jena" was one of several works by Meissonier included in its catalogue; however, "1806, Jena" was not actually displayed, reportedly because it was unfinished. It would take the notoriously meticulous Master three more years to finish his last great Napoleonic canvas. Meissonier eventually displayed the still unfinished "1806, Jena," at the inaugural salon of the Société Nationale des Beaux-Arts in May 1890. He died seven months later in January 1891.
Correspondence in the Meissonier family archives suggests that the painting was commissioned by Edmond Simon, an art agent in France for the London firm of Arthur Tooth & Sons. The painting entered Simon’s possession by 1893, when he lent it to the posthumous Meissonier retrospective at the Galerie Georges Petit in Paris. "1806, Jena" later traveled to Pittsburgh, where, following its inclusion in the 1896 Carnegie Annual, it was purchased by industrialist Charles Lockhart.