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Although Kearny had superior orders from the United States War Department, he had previously sent most of his troops back to Santa Fe, New Mexico, believing that the war in California had ended, and his remaining force sustained heavy losses in the United States defeat at the Battle of San Pasqual.
For his contributions to military medicine in the Second World War, he received a second Distinguished Service Medal with Oak Leaf Cluster, the Legion of Merit from the United States War Department, the Order of the British Empire by King George VI of Britain, the Croix de Guerre by the French government, the Companion of the Order of the Bath, and Chevalier of the Légion d'honneur.
For a time he was consulting engineer to the United States War Department in respect to the railroads of the Philippine Islands.
The U.S. Military Railroad (USMRR) was established by the United States War Department as a separate agency to operate any rail lines seized by the government during the American Civil War.