At the outbreak of the American Civil War, Johnston was the commander of the U.S. Army Department of the Pacific in California. Like many regular army officers from the South, he was opposed to secession. But he resigned his commission soon after he heard of the secession of the Southern states. It was accepted by the War Department on May 6, 1861, effective May 3. On April 28 he moved to Los Angeles, the home of his wife's brother John Griffin. Considering staying in California with his wife and five children, Johnston remained there until May. A sixth child was born in the family home at Los Angeles, where his eldest son, Capt. Albert S. Johnston, Jr. was later killed in an accidental explosion on a steamer ship while on liberty, in 1863.