Mark Perkins, who was Shepherd chief executive, took up the role at Wates of managing director of SES Engineering Services after the merger in October.
Wates said it was presently working through a succession plan to find his replacement.
Andrew Davies, Wates Group chief executive, said: “Having played a key role throughout the Shepherd acquisition process, Mark Perkins has decided to pursue the next stage of his career outside the Wates Group.
“Consequently Mark will step down from his role as managing director of SES Engineering Services with effect from the end of May.
“Mark has made a substantial contribution to the growth of SES since he joined the Shepherd Group in 2002. On behalf of the Board and senior management team, I would like to thank Mark for his dedication and professionalism and wish him well in his future endeavours.
“We are currently considering the succession plan for the role of managing director of SES and this will be the subject of a further announcement in due course.”