Lt. Gen. Franklin L. "Buster" Hagenbeck, the retiring West Point superintendent, will pass the command to Huntoon during a ceremony overlooking the Hudson River on Monday.
Huntoon has been director of the Army Staff in Washington, D.C.
The 1973 West Point graduate was involved in Operation Desert Storm and was commandant of the U.S. Army War College.
Hagenbeck became West Point superintendent in June 2006. He previously commanded the 10th Mountain Division, based at northern New York's Fort Drum. His troops helped spearhead a victory over al-Qaida and Taliban militia fighters in Afghanistan as part of Operation Anaconda in March 2002.