Sue Baldwin, the director of school efficiency at the DfE, will take over from Tim Coulson on 1 August.
She will become the 13th person to have taken up one of the eight commissioner roles in England since they were introduced in summer 2014.
RSCs oversee the academy system in their regions, with powers that include approving applications for new academies and free schools, intervening in under-performing academies and deciding the fate of coasting schools.
'Experience and talent'
The high turnover of RSCs – many move to jobs with academy trusts – has led to concerns about the stability of the system, and whether the role is well-suited to the headteachers and academy figures who have usually been appointed in the past.
Ms Baldwin said: “I am delighted to be appointed as regional schools commissioner for the region where I live and where my wider family has long-standing connections. I want to make sure that every child and young person has the best school place possible and that they are excited by the opportunity that a brilliant education can offer.”
National schools commissioner Sir David Carter said: "I am thrilled that Sue Baldwin is joining my team as the new regional schools commissioner for the East of England and North East London region.
"Sue will bring a wealth of experience and talent from her recent roles as the department's director for academies and maintained schools and school efficiency.
"Sue has an excellent understanding of the schools system and its future development, and a passion for education which will make her a really strong appointment.”