After graduating from the United States Military Academy, Wharton’s assignments have included inspector general to the U.S. Army Western Command at Fort Shafter, served as battalion S-3 in the 25th Supply and Transport Battalion, 25th Infantry Division (Light), Schofield Barracks, was the Lieutenant Colonels' Assignments Officer at the U.S. Army's Personnel Command, and battalion executive officer in the 210th Forward Support Battalion, 10th Mountain Division (Light Infantry) and later deployed to OPERATION RESTORE/UPHOLD DEMOCRACY as the Battalion Commander (Forward). He also served as chief, Division Materiel Management Center, 10th Mountain Division Support Command, a joint Strategy Planner in the Logistics Directorate, J-4, Joint Chiefs of Staff, commander of the 1st United States Army Support Battalion, 507th Corps Support Group (Airborne), MFO, Sinai, Egypt, and the quartermaster branch chief at PERSCOM.
In 2001, Wharton assumed brigade command of the 55th Theater Support Command (AC/RC), Eighth United States Army. He later led the CSA's Task Force Logistics, was the Deputy Commander (Futures), U.S. Army Combined Arms Support Command, director, Army Initiatives Group, Army G-4, and executive officer to the HQDA Deputy Chief of Staff for Logistics, G-4. He was deployed to Kuwait as commanding general, AMC-SWA/ U.S. Army Central G-4/CFLCC C-4 for Operations Iraqi Freedom and Enduring Freedom, was the U.S. Army Materiel Command chief of staff and served as the commanding general, U.S. Army Sustainment Command and Rock Island Arsenal, and as the senior commander for U.S. Army Garrison.
He most recently served as commanding general of the U.S. Army Research, Development and Engineering Command.