On Tuesday he was given a warm welcome at the base in his new role as Royal Honorary Air Commodore, a position he took over from his father King Charles in August last year.
The site is the RAF's only station in Wales and is home to the No 4 Flying Training School, responsible for training the UK's next generation of fighter pilots. Crews at the base are also trained for mountain and maritime operations across the world.
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Take a look at the best photos from the visit…
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A warm welcome
Prince William was given a warm welcome as he arrived for his official visit. Braving the rain, the royal stepped out with a smile, dressed in a navy suit, a striped tie and a crisp shirt.
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A light-hearted moment
Despite the grey clouds and rain, Prince William could be seen laughing as he shared a light-hearted moment with a member of RAF Valley.
"It wouldn't feel like home if I wasn't back here on a day like this," he quipped.
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Air Traffic Control tower
William was given a tour of the base and met personnel from across the station, who told the royal about their work and day-to-day life at the RAF Valley.
The first stop of the day was at the Air Traffic Control tower, where William, 42, saw the control rooms and new surveillance equipment.
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RAF Valley plans
He was also told about plans to refurbish RAF Valley's second runway in a project estimated to cost around £44million.
And looking out to Llyn Peninsula, William said: "It's a bit of nostalgia for me."
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Fire and Rescue Section
At the base's Fire and Rescue Section, William met crew members who work to provide year-round airfield rescue firefighting and structural firefighting cover for RAF Valley, whilst also delivering further support at the station's relief landing ground, RAF Mona.
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Fighting fire
The Prince took part in a simulated fire response exercise, sitting in the passenger seat of a fire truck and operating the hose to drown out the flames on an "iron hawk" jet used for practice drills.
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Action hero
He looked to be having great fun, taking part in the drill.
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Warming up with a cup of tea
Next it was time for William to meet engineers, Qualified Flying Instructors, and trainees in their crew room - with a cup of tea in hand, of course.
William's mug was aptly emblazoned with his title 'HRH Prince of Wales'.
He was reunited with his former flying instructor, Captain Brian Wills, who said: "It was great, really nice to see him. The last time I saw him was 2009.
"I get asked a lot how was it training him and what extra privileges did he have, but I treated him like anybody else. He did everything exactly as anybody else would have done."
He said the prince had stayed in touch, sending a bottle of whisky and a birthday card when he turned 50 two years ago.
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Presenting awards
He was also given the honour of presenting the annual Prince of Wales award to the best Qualified Flying Instructor, Flight Lieutenant Jake Fleming.
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Inspecting aircraft
Heading back outside, William was shown a RAF Short Tucano trainer aircraft.
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RAF Mountain Rescue Service
He also chatted to the response team from the RAF Mountain Rescue Service (MRS), which is on call 365 days of the year and provides vital, life-saving support to the local area.
Last year, the MRS were called out 25 times, often operating in severe weather conditions with near-zero visibility.
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Well wishes for wife Kate
Before leaving, William had the chance to meet families of those stationed at the Valley.
He also caught up with Rita Millan, who has worked in the Thrift Shop on the base for 20 years. "We used to see him all the time time passing in his car and he used to wave," said Rita. "He said he loved coming back to visit us.
"I said to him I hope Catherine is on the mend and we're praying for her and to send her our love. He said he would tell her."
Her colleague Denise Stock added: "He said he misses it here."
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Chatting to kids
William also enjoyed a chat with a group of children, who all proudly waved Welsh flags.
He asked them their names and when one girl said her name was Charlotte he replied: "I know one of those!"
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Little ones
The father-of-three looked particularly taken by one baby who was snoozing in a buggy and bonded with one mother over sleep regressions.
LISTEN: The King's special relationship with the Prime Minister revealed
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