Stephen McDonald, who was appointed in August last year, is to leave after "mutual recognition that there was a difference in expectations over the balance of the role", according to a council statement.
The statement added that the decision was not "a reflection of Stephen’s perfomance in his short time with the council".
"The authority is grateful to Stephen for his contribution and for having the foresight to recognise that the scope of the role was not playing to his strengths in the way the council and he hoped it would," the statement said.
The statement also said that, due to the "disappointing outcome" of McDonald’s appointment, it would not rush into making a "like-for-like" appointment.
In the meantime, the council’s three divisional directors will report directly to the chief executive.
McDonald joined Croydon from the London Borough of Hackney where he was director of regeneration, with his remit covering the Olympic legacy.
When McDonald joined Croydon, a statement from the local authority said he would be responsible for planning and building control, regeneration and economy, environment management and public safety.
At the time of the announcement of his new role with Croydon, McDonald said: "I’m genuinely excited at the prospect of picking up the planning and environment reins at such a pivotal moment for Croydon."
"I’m aware of the fantastic work that’s been done by the team to get the town to this point, and am confident that I can lead the next stage and help guide the successful implementation of the plans that will revitalise the borough."
Prior to joining Hackney, McDonald was strategic director of major projects at the London Borough of Southwark.