Crainey was initially in charge of the club on an interim basis in December following the departure of Simon Grayson but a bright start to life at Higbury led to him being given the role until the end of the season.
Now, however, the club have decided that he will return to his former role with the U23s, where he has received high praise throughout his time on the Fylde coast.
Under the 40-year-old, the Cod Army survived in League One on goal difference. He won 26 points from a possible 78 whilst in charge though his remit when being given the head coach role was to keep the Cod Army in the division, which he acheived.
Fleetwood owner Andy Pilley said: “We’d like to thank Stephen for guiding the club to safety and the commitment he’s shown to the cause since taking charge of the first team. The development of players is hugely important to the club, and that’s something we want Stephen to continue with his role in the Under-23s.”On finding a new head coach, he continued: “This isn’t something we are going to rush.“We intend to take our time to ensure we find the right person to take the club forward and over see what will be a hugely important summer for Fleetwood Town. We have now started the managerial recruitment process”