Commenting on the move, Allen Clarke said: "It has been an honour and a privilege for me to have been involved in such a critical role for Irish rugby over the past five years.
"I have worked with extraordinarily dedicated people across committees and team managements, but above all else so many of the young players I have come in contact with have been truly exceptional in their dedication and desire to progress to the highest levels.
"Ulster Rugby has done extraordinary work, both on and off the field, to develop rugby in the province and is positioned for further major growth and success in the coming years.
"I look forward to being a part of this dynamic unit and contributing to what will undoubtedly be an exciting time for Ulster Rugby."
Eddie Wigglesworth, IRFU Director of Rugby, said: "Allen has done a tremendous job of developing the age grade representative structure and, indeed, the entire elite player development pathway within Irish rugby.
"The fruits of his work have been seen in the success of Ireland's underage teams over the past number of years and, more particularly, in the number of talented young players who are coming through into the higher levels of the senior ranks.
"It is heartening to see he is staying within the Irish rugby family and we wish him every success in his new career."
David Humphreys, Director of Rugby at Ulster Rugby, in welcoming Clarke's move to Ulster, added: "We are delighted to welcome Allen to our High Performance Academy and look forward to him building on the superb work already undertaken by Gary Longwell.
"Ulster Rugby recognises the critical importance of investing in the future by developing talent from within and we have, and will continue to devote significant resources in terms of finance, facilities and personnel to this area.
"The team of Gary Longwell, Brian McLaughlin and now Allen Clarke will ensure that we deliver, and maintain, a world class High Performance Academy programme which will be an integral part of delivering on Ulster Rugby's ambitious targets."