Fighting with Maj. Gen. Winfield Scott's army in the Mexican–American War, Stone was promoted to second lieutenant on March 3, 1847. He first saw action during the siege of Veracruz from March 9–29, then the skirmishing near Amazoque on May 14, and the Battle of Contreras on August 19–20. Stone then fought notably during the Battle of Molino del Rey on September 8, and was appointed a brevet first lieutenant from that date for "gallant and meritorious conduct" in this fight.