Obama praised McHugh as "a distinguished public servant who will help keep us safe and keep our sacred trust with our soldiers and their families."
McHugh, a Republican who represents constituents in far-northern New York State, which includes the Army base at Fort Drum, is the senior member of his party on the House Armed Services Committee.
"John has proven himself a dedicated representative of the people in northern New York," Obama said. The 10th Mountain Division that's based at Fort Drum, he said, is the most-deployed division in the U.S. Army.
McHugh "is committed to keeping America's Army the best-trained, the best-equipped (and) the best-led land force the world has ever seen," Obama said.
The president noted that McHugh's father served with distinction aboard a B-17 bomber during World War II, while his mother cared for wounded servicemembers through the Nurse's Corps.
McHugh said he is "enormously moved and deeply proud" to be nominated as the next Secretary of the Army.
The Army has "always had a special place in my heart," McHugh said.
McHugh's nomination must be approved by the U.S. Senate.