On March 3, 1847, Hébert accepted a commission as a lieutenant colonel of the U.S. 3rd Infantry Regiment, and then on April 9, 1847 he was transferred to the U.S. 14th Infantry Regiment. As a lieutenant colonel of the U.S. 14th Infantry Regiment he fought at Contreras, Churubusco, Molino del Rey, Chapultepec and Mexico City. At Molino del Rey he was honored by General Winfield Scott and was brevetted a Colonel for bravery. He was cited for gallantry at Chapultepec and Mexico City. Discharged on July 25, 1848, in New Orleans, Colonel Hébert entered politics.