The comprehensive school in Bermondsey saw off strong competition from 13 other shortlisted schemes to clinch the prestigious prize at a ceremony last night.
The award, which is backed by CABE and the Office of Government Commerce, attempts to reward procurement and construction as well as the design quality.
Since opening at the beginning of this academic year, the City of London Academy has proved extremely popular, with 1,370 pupils applying for 180 places last year.
Studio E's designs for the school, which was sponsored by the City of London, enjoy many of the facets that have become familiar in the typology of city academies, such as a 'light and airy atrium at its heart' and a 'dramatic entrance and social hub'.
Speaking last night, CABE chair John Sorrell defended the academies programme, which has been under attack from some quarters in the last 18 months.
'It is interesting that academies appear to enjoy considerably better design than other schools,' he said. 'The key difference appears to be not just cost but the extra time for design and consultation in the early stages of the project.'