Shane Logan is to stand down from his role in August after eight years of being chief executive officer of Ulster Rugby.
A recruitment process to find his successor will now begin, in light of the news.
"I am very grateful to have had the privilege of being chief executive of Ulster Rugby since 2010," Logan said in a statement on the province's official website.
"In terms of win ratios, the senior Ulster team has become more competitive but I am as disappointed as anybody not to have landed that elusive trophy."
IRFU chief executive Philip Browne said, "We thank Shane for his dedication to Ulster Rugby and are sorry to see him go, but wish him all the very best for the future."
Logan has not yet commented on why he is stepping down from his position.
It comes, however, after a testing year for Ulster, which included the high-profile rape trial involving Paddy Jackson and Stuart Olding.
Both were found not guilty of charges against them but the pair had their Ulster and Irish Rugby contracts revoked in April for other aspects of their behaviour.
It also follows the departures of director of rugby Les Kiss and head coach Jono Gibbes earlier in the year.