Owners Fenway Sports Group, led by John Henry and chairman Tom Werner, have also made Damien Comolli the club's director of football - a step up from his position as director of football strategy.
The search for a managing director has taken FSG longer than they had anticipated as when they began the hunt in December they hoped to have a man in position early in the new year.
However, Ayre's appointment is recognition of the impressive work he has done on the commercial side since he joined the club in July 2007.
Source: PA