Rowley was also present during the Vicksburg Campaign during the late spring of 1863. He was appointed Lieutenant Colonel and Military Secretary on Grant's Staff, when Grant assumed the rank of lieutenant general on March 2, 1864. He remained in that position until his health began to fail, in October of that year, after the Wilderness campaign, forcing him to resign from the army. Rowley was one among nine Civil War generals that came from Galena, Illinois.