Within his role he has also installed and tasked his management team to oversee the department's remit to develop both the elite and community game in Wales.
The rugby pathway structures are managed by Gethin Watts as National Performance Manager, Jason Lewis, National Development Manager tasked to oversee grassroots rugby with Rob Yeman as Match Officials Manager and Allan Lewis as National Academy Coaching Manager.
Joe Lydon is to become the Head of International Player Development for the Rugby Football Union.
During his time in Wales the former Rugby League star's Rugby Department has:
* restructured the player pathway which leads into the national squad
* helped create a development region in North Wales
* played a pivotal role in the creation of the WRU National Centre of Excellence
* tasked some 52 full time WRU staff with focusing on the community game
* implemented a restructure of the Principality Premiership and helped launch the British & Irish Cup.
* helped manage the relationship with the four Regions through the Participation Agreement
* championed the development of the Wales Sevens squad and revitalised the U20, U18 and U16 national squads.
Lydon arrived in Wales with a rugby CV which included 32 GB rugby league caps, experience as Technical Director of the Rugby Football League and a background in the union game as England Sevens and then senior team backs coach.
He said: "I am sad to be leaving Wales, but the challenge of playing such a pivotal role in the development of English rugby at this time is one I had to take up.
"Welsh rugby is in great shape and I leave behind a team of people more than capable of achieving the goals we have set.
"The experience I have gained across the past five years with the WRU will set me in great stead for the exciting new challenge ahead.
WRU Group Chief Executive, Roger Lewis, said: "I am personally and professionally sad to see Joe leave but the whole of Welsh rugby will always be grateful to him for what he has achieved during his time in Wales.
"In Joe we chose the right man to introduce an unprecedented scale of change and reform which had to be achieved for the continued growth of our game.
"The reforms he has helped introduce mean we now have a clear vision of the way forward and the structures in place to achieve our objectives.
"During our next phase of development we will be making sure that all the important relationships thrive across the game so that we can work together to protect and develop rugby in Wales at all levels.
"Joe leaves with our gratitude for what he has done and our best wishes for the future in his new role."
The WRU has already launched its search for a replacement for Joe Lydon who will take up his new role with the RFU at a date to be confirmed.