Cooper, 34, will report into England Under-21s Head Coach Gareth Southgate and The FA’s Director of Elite Development Dan Ashworth, after taking up the role with immediate effect.
The U16s start their Victory Shield campaign with two away games against Wales and Northern Ireland before playing host to Scotland at Yeovil Town’s Huish Park on Thursday 20 November.
Cooper joined The FA from Liverpool’s academy, assuming the post of FA Youth Coach Educator (FAYCE) in 2013.
Until this month, Cooper was one of 18 FA Youth Coach Educators working in club academies across the country, helping support the Elite Player Performance Plan develop the next generation of young players.
In 2007, he became one of the youngest coaches to achieve a UEFA Pro-license qualification aged 27.
Speaking about his appointment, Cooper said: “I am very proud and privileged to have been offered the role of U16 Head Coach in what I think is a really exciting time for youth development football in this country.
“I’ve been fortunate to work within The FA for a year now, working with all the professional clubs as a youth coach educator. This is something I really believe in and I hope to help evolve in the future.
“The FAYCE is a really important programme within youth football and has given me an insight into all the good things that The FA is doing and all the good intentions that are being made towards developing elite footballers.
“I’m really honoured and excited to get the role but this is not about me, my priority is to provide the best opportunity to the best young players in the country to maximise their development and progression.
“At this age group we have to be conscious of the players age and it is still very much at looking at the players and their future potential and their performance levels. We want to create the right environment for the players to develop by playing exciting attractive football that fits into the future of England’s philosophy.
“I will be working very closely with all the national coaches, building on all the good things that is happening under Dan Micciche at U15s level and getting them prepared for when they work with John Peacock in the U17s setup.
“Getting the players ready for the future is the aim and preparing them for the next levels of their careers, eventually with the ending view which is producing players for the senior team.”
Gareth Southgate added: "Steve joins our National Coaches having impressed us all with his work as an FAYCE over the past year.
"He has a clear understanding of elite young players and an elite environment from his time at Liverpool working with the likes of Raheem Sterling, John Flanagan and Andre Wisdom.
"He has also benefitted from working with the Spanish influence that was present in Liverpool's youth set up at that time.
"Steve matches our values and philosophy but also brings new ideas and an impressive attention to detail. We look forward to working with him as a group of National Coaches."
Cooper started his playing career at Wrexham, playing as a professional for two years from 1998, before moving into coaching in 2001.
He became Wrexham’s head of youth and youth team coach in 2006, then joined Liverpool in 2008
He spent five years at the Anfield club, serving as head coach at for players aged 6-11 and later 12-16, before taking the post of Academy Manager in 2011.
Tickets for Cooper’s first home match in charge of England U16s against Scotland, on Thursday 20 November, kick-off 7.30pm at Yeovil Town’s Huish Park are on sale now, priced at £3 adults and £1 for children or OAPs.
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