On the outbreak of the Civil War in April 1861, he was appointed Flag officer of the Atlantic Blockading Squadron. In August he was sent with troops under General Benjamin F. Butler, to capture two coastal forts near Cape Hatteras. In the ensuing battle, the fortifications were captured without loss, though not without some difficulty owing to the weather, and the fleet returned to Fort Monroe to general acclaim. However this soon give way to criticism of Stringham for not taking his ships closer in, and continuing to attack along the coast. The fact that his ships drew too much water to enter the shallow coastal waters, and that he had been directly ordered to return immediately, eventually emerged, but apparently too late to soothe his irritation, as the next month, at his own request, he was relieved of his command. As some small compensation on August 1, 1862 he was promoted to the rank of rear admiral on the retired list.