The firm will develop phase one of the £42.9 million Pembroke Learning Campus.
Works on the first stage includes creating a new 1,463 place 11-18 secondary school and autism centre for 30 learners.
The overall project is part of the council's £149m 21st Century Schools Capital Programme.
In addition, Gleeds has been appointed to providing cost and project management services on the scheme.
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Construction is expected to begin this month, with an opening date scheduled for September 2018.
Work will then begin on demolishing the old school and forming new external areas, with construction due to be completed by May 2019.
Bouygues UK's Regional MD, Chris Stevens, said: "We're excited to be working on the new Pembroke Learning Campus - it will be a fantastic new educational facility for local schoolchildren and builds on the council's commitment to improving schools, providing modern learning environments for the benefit of children for generations to come.
Pembroke School head teacher, Frank Ciccotti, added: "The governors and staff are delighted that the contract has been issued and so the work on delivering Phase 1 of the Pembroke Learning Campus is finally underway after four years of detailed planning."
(LM/MH)
