The position has been vacant since Jonathan Ford departed in March after a vote of no confidence was passed by the FAW council ahead of the Red Dragons’ matches against Belgium, Mexico and Czech Republic.
But former League of Ireland player Mooney – who is currently UEFA’s head of strategic development – has landed the huge role in the Welsh setup.
He will begin his new post on August 30 ahead of Wales’ friendly against Finland and their 2022 World Cup qualifiers with Belarus and Estonia in September.
“In this next chapter for Welsh football, we will grow and evolve the game to become more popular and successful,” said the Irishman.
“The mission is very clear and I can’t wait to work with everyone in Welsh football to reach our full potential.
“I have enjoyed collaborating with great people to grow European football at UEFA for the past decade and now the focus will be on ensuring that the FAW becomes one of the best football associations globally at all levels by being strong locally in every village and town across Wales.”
Mooney – who hails from Cappamore, Limerick – was tasked with improving domestic football in Ireland after earning a job with the Football Association of Ireland in 2006.
The former Limerick, Cork City and Shamrock Rovers goalkeeper went on to market the League of Ireland.
Mooney has been with UEFA since 2011 and was seconded to the FAI for six months in 2019 to lead the association ad interim.
Speaking about Mooney’s impending arrival, FAW president Kieran O’ Connor said: “The FAW have identified Noel as the right person to manage the FAW into a new era of success and evolution.
“He has a vast experience of working across all European national associations over the past decade to grow European football and we are delighted that Noel has agreed to focus his experience and skillset to develop football in Wales.”
Mooney’s appointment comes amid a significant period of uncertainty for the national side.
Rob Page has taken charge of Wales since Ryan Giggs was arrested in late 2020 on suspicion of assault. The Manchester United legend denies the allegations against him.
Page led Wales to the last-16 of Euro 2020 and is expected to be at the helm for the remaining matches in 2021.
Giggs – who is accused of deliberately headbutting his ex-girlfriend Kate Greville, 36, and controlling her throughout their relationship – will face trial at Manchester Crown Court on January 24 next year.