The awards, held at London's Grosvenor House Hotel, celebrate innovation and excellence in the UK's education industry.
Manchester was singled out from a shortlist that included Westminster, Essex, Knowsley, Leicester, Sheffield, Southwark and Waltham Forest.
The judging panel was made up of industry experts including Sir Bruce Liddington, director general of E-ACT and former schools commissioner, Susan Anderson, director of public services, CBI and Andrew Haldenby, a director at Reform.
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Manchester's BSF programme was praised by judges saying they were "impressed by the scale and ambition of Manchester's BSF programme, as well as the enthusiasm of its community and the degree of challenge it faced".
Councillor Sheila Newman, Manchester City Council's Executive Member for Children's Services, said: "As a city, we are extremely proud of the delivery of our BSF and Academies programme. We are providing young people and our communities with high quality, innovative and inspirational learning spaces that will foster self confidence and give children and young people a positive start in life with the skills and qualifications to become active citizens today and in the future."
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