The planned 10,000 square metre secondary school will be located in a building reaching up to nine storeys in height which is currently occupied by various Government departments.
The planning application was made by the charity Oasis Community Living. The charity last summer won a bid to open a secondary school under the Government's free school initiative.
The Council's planning officers said in their report (19-page / 284KB PDF) that the proposed conversion was acceptable as it retained employment use on the site.
"It seeks to make good use of the existing building, adapting it for its own purpose with minimal impact on the external appearance," the report said.
"I am thrilled that Oasis has been given the opportunity to open a brand new secondary school in Waterloo," said Oasis founder Steve Chalke when the Government accepted its application last year.
"This marks the start of an exciting new chapter for the area as we work with many business and community partners to develop an innovative curriculum as well as a wide range of extra-curricular enriching activities for local young people," Chalke said.
The planning permission is subject to the conclusion of a section 106 agreement. Oasis has said it hopes to open the school in September this year.