Lesley Reid will leave next month after two years at the helm. Plymouth chief executive Mike Robinson will run the department directly until a replacement is found.
Reid said: "Now is a good time for someone else to come in to take over and I know the department will continue to thrive."
In December, Plymouth was the only council to drop into the Audit Commission's "poor" category. This was partly blamed on a rock-bottom one-point score for children's services.
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