Harry, 28, served as a co-pilot gunner in the attack chopper during his 20-week tour in Afghanistan's restive Helmand Province, which ended in January.
Harry -- who will be overtaken as third in line to the throne by his brother Prince William's first baby, due this month -- passed the commander test earlier this week.
The second son of Prince Charles, the Prince of Wales, Harry is serving in 3 Regiment Army Air Corps.
"This is a tremendous achievement for Captain Wales who passed with flying colours," said Lieutenant Colonel Tom de la Rue, his commanding officer.
"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."
The qualification is the culmination of three years of training and experience in the Apache.
Since returning from Afghanistan, the prince has gone through several months of training, flying day and night missions in Britain, to prepare for the six-hour test for his upgraded role.
He was required to plan and deliver patrol orders, navigate throughout, fly in a controlled airspace and conduct a simulated low-level attack on the Spadeadam airbase in northern England.
He also had to manage several diversions and simulated aircraft emergencies.
A few weeks before flying out to Afghanistan in September last year, the royal was pictured frolicking naked during a weekend break in Las Vegas.
Harry said during his tour that he had killed Taliban fighters, who were taken "out of the game" by his unit if they targeted British soldiers.
Harry will continue with his normal duties as an Apache pilot based at Wattisham Airfield, near Ipswich in eastern England.
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