The builder will deliver the £12m Priory Ruskin Academy at Grantham and the £9m University Academy Holbeach for Lincolnshire County Council.
The wins mean contracts have now been signed for the first 16 academies released by the Government after the schools reviews.
Balfour Beatty is top of the form with seven academy wins. These are: The Bourne Academy, Bishop of Winchester and Oasis Academy Hadley. In the south east and East Anglian region Balfour also won Ipswich, King’s Lynn, Thetford and Felixstowe academies.
Along the south coast, Kier has picked up jobs for Eastbourne and St Leonards academies.
Wates also walked off with two jobs, winning De Warenne Academy and Outwood Academy in Doncaster.
Bam scored successes bidding for Kearsley Academy in Bolton and Aylesbury Vale Academy.
Apollo and McAlpine have so far picked up one job each, at the Portslade Aldridge Community Academy in Brighton and Sarum Academy in Wiltshier, respectively.
Shepherd said building work on the Priory Ruskin Academy will start next February, subject to planning permission being granted.
While the University Academy Holbeach will get underway in April.
Peter Bates, programme director for Shepherd Construction said: “We’re delighted to have won this contract and look forward to delivering facilities that will match the vision for both academies by providing an ideal learning environment that will promote achievement, personal development and opportunities for progression.”
Councillor Mrs Patricia Bradwell, Executive Councillor for Children’s Services, said: “The academies in Grantham and Holbeach have been waiting to progress with building plans and with the preferred bidder now in place, they can look forward to deciding on designs before they begin to take shape in early 2012.”