The Italian's future at the club has been the subject of much speculation following a poor run of results but the Nerazzurri chief has offered him his full support
The young boss's future was thought to be in question, with the Nerazzurri slipping to seventh spot before Sunday's 1-0 win over Parma, a victory that elevated them back into fifth.
"The project will start again with Stramaccioni," Moratti told Sky Sport Italia.
"You always ask me whether he'll stay and I always tell you yes.
"It is not easy to plan for the future if your computer has a virus, when you have had as many players injured as we have, but we are thinking about next season and doing that well."
The 67-year-old publicly supported both Alberto Zaccheroni and Roberto Mancini before they parted company with the club, but Moratti insists his backing of Stramaccioni is genuine.
"Zaccheroni and Mancini were different situations. Roberto decided to leave and then what happened, happened," he explained.
"We needed to look for a new coach even if Mancini had done really well and we therefore went to Jose Mourinho. But it was Mancini who broke away."