Ian Thomas, who took over as director of children's services in Rotherham in January 2015, will become chief executive of Lewisham Council.
The news comes little more than a month after children's services in Rotherham were rated "good" by Ofsted, three years after being judged "inadequate".
Rotherham Council said deputy strategic director Mel Meggs will step into the post in an acting capacity when Thomas leaves, while the council seeks to recruit a permanent replacement.
Chief executive of Rotherham Council Sharon Kemp said: "Ian has led children's services through their improvement and has achieved many changes, taking them from being rated as inadequate by Ofsted three years ago to the recent overall good rating, with outstanding features.
"He leaves the service and the council in a very good place and we are confident this will enable us to seek a replacement of equal calibre as quickly as we can."
Rotherham Council said a leaving date for Thomas is yet to be negotiated but is expected to be within the next three months.
Thomas said: "It is with heavy heart that I say goodbye to Rotherham Council as I have enjoyed being here and being part of an amazing team. They are the ones who have helped to turn around children's services and I know they will be in good hands under Mel while a new strategic director is sought.
"There is continued commitment to improvement and I know the staff are the right people to help lead the necessary further changes to help protect Rotherham's most vulnerable children now and in the future.
"I also want to thank the leadership here and elected members at the council for helping drive forward the many changes we have seen over the last few years.
"This has been a team effort and Rotherham Council is definitely a much better local authority today than the one I joined three years ago and the people of Rotherham should be proud of what has been achieved in such a short space of time."
