The 49-year old Englishman was appointed by the Sky Blues in May but after just six matches of the 2012/13 season has decided to end his tenure at the Sydney Football Stadium.
"I've decided to stand down as Head Coach of Sydney FC," Crook said. "It's something I've been thinking about for a few weeks now. I love coaching and I love this club but the head coach role is just not for me.
"I always said that if the role started to affect my personally or my family or my ability to sleep at night I would make a change and that was happening so I wanted to do the right thing by the club.
"This is a great club and the Head Coach role is a fantastic job but it just wasn't for me. It has been a privilege to coach Sydney FC and I don't regret it for a second but I just felt it was the right thing to allow someone else to take over now so they have time."