In July 1861 a regiment known as the Engineer Regiment of the West recruited mainly in the States of Illinois and Missouri, was organized by Col. J. W. Bissell, and Henry Flad was made captain of Company B. In August of the same year he was detailed by General Frémont, then in command at St. Louis, for service in the construction of fortifications at Cape Girardeau, Missouri, where he remained for several months. Later in the year, when Frémont was succeeded by General Halleck, Captain Flad was ordered to join General Pope in southeast Missouri, and served as a staff officer through the campaign of New Madrid and Point Pleasant and the taking of Island Number Ten, after which he rejoined his regiment at New Madrid. He was with his regiment at Fort Pillow and Pittsburgh Landing and in the operations before Corinth. During the summer of 1862 he was engaged in repairing the Mobile and Ohio Railroad, in building forts at Corinth, and in repairing the Mississippi Central Railroad. He was also engaged in Grant's advance on Grenada. In February, 1863, he was ordered to Young's Point, where he was employed in engineering work, as he was later at Baxter Bayou, Lake Providence, and Bayou Macon.