In July 1861, O'Rorke served at the Battle of Blackburn's Ford and the First Battle of Bull Run, where his horse was killed from under him, and then as assistant engineer in preparing the defenses of Washington, D.C. He sailed with the Port Royal Expedition in October 1861 and provided vital reconnaissance and engineering in constructing the batteries on Jones, Bird, and Tybee Islands for the bombardment and siege of Fort Pulaski, on Cockspur Island near Savannah, Georgia. Following the capture of the fort on April 11, 1862, O'Rorke was selected as one of the officers to receive the surrender.