Pendlebury, 36, joins the RFU from Wasps Rugby where he was regional academy manager.
He also played for Gloucester but spent most of his career in the Broad Acres starting at hometown Rotherham when they were in the Premiership and having a four-year stint at Carnegie before injury forced his early retirement in 2012.
Nevertheless, Pendlebury joined the coaching set-up at the Headingley club, first assistant academy coach and later academy manager, where he had five players in England’s winning squad at the 2016 World Rugby U20 Championship.
He moved back to the Premiership with Wasps as academy manager in 2017 but now joins the governing body.
“I’m really honoured and excited to be taking on this role with England Rugby and helping guide the next generation of talent coming through the international player pathway,” he said, having played for the England age-groups himself as a teenager.
“I’ve thoroughly enjoyed my time at Wasps where, as a team, we’ve managed to develop and help a lot of fantastic young players progress through the system.
“I’m really proud of what myself and the Wasps Academy have achieved over the past couple of years and I’d like to thank the club and wish them the best of luck in the future.”
As well as taking the national side, Pendlebury will work with schools and the 14 regional academies to help identify and develop the next generation of England players.
Head of professional rugby Nigel Melville said: “The U18s along with our U20s men squads are very important teams for the future of the senior national team and we are seeing significant transition through the pathway.
“Jonathan’s knowledge of the academy space and relationship with the other academies and schools is going to be crucial in the recruitment and development of the next generation of England players.
“He is an excellent coach and passionate about this age group and the development of young players.
“He has a larger pool of players to work with so part of his role will be getting players through the Player Development Group (PDG) and into England U18s.”