While it does not mark a change in his rank as Captain in the Army Air Corps, the qualification means he can now take overall control of the helicopter on missions.
"This is a tremendous achievement for Captain Wales, who passed with flying colours. I am delighted that his new status as a qualified Apache aircraft commander and co-pilot gunner places him at the very top of his profession," said his commanding officer, Lieutenant Colonel Tom de al Rue.
The third in line to Britain's throne passed after undergoing a six-hour assessment earlier this week, including a simulated attack on RAF Spadeadam in Cumbria.
The assessment comprehensively tested his ability to perform as an aircraft commander across a wide range of tactical and procedural scenarios.
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Earlier this year, the 28-year-old had completed a five-month tour of Afghanistan as a co-pilot gunner.
During his deployment in Helmand, the Prince - known as Captain Wales in the Army - shared flying duties and took control of the weapons of the two-man Apache.
Harry was awarded a prize for best co-pilot gunner when he first qualified as an Apache pilot in February 2012.
A Kensington Palace spokesperson confirmed that the Prince "will continue with normal duties as an Apache pilot based at Wattisham Airfield".
Harry serves in 662 Squadron, part of 3 Regiment Army Air Corpos, which in turn is part of 16 Air Assault Brigade's Attack Helicopter Force.