During the Civil War, he commanded gunboats Commodore Perry and Miami in operations in the North Carolina sounds. He was killed in action on April 19, 1864 in Albemarle Sound in an engagement between Miami and the ram CSS Albemarle, which had been disruption operations of the Union fleet from its base at nearby Plymouth on the Roanoke River. In that action, Flusser personally fired a cannon shell at the Confederate ironclad. The shell, with a 10-second fuse, bounced off the Albemarle’s armor and landed back on the deck of the Miami, where its explosion killed him.
Brigadier General Henry Walton Wessels, commanding Union Army troops facing Plymouth, noted: “In the death of this accomplished sailor the Navy has lost one of its brightest ornaments.”