Willmott Dixon will install modular buildings as extensions at Eresby School in Spilsby and Willoughby School in Bourne.
Eresby School will get more classroom space, a hall for rebound therapy, hygiene suite facilities, an IT suite and science lab, calm rooms, physio space and staff rooms.
Willoughby School will get classroom space, hygiene suites, a dining hall, and nurse and physio spaces.
At both sites, landscaping works include extending the car parks.
The work is due for completion in November 2021.
Lincolnshire County Council plans to spend £86m on improving its SEND school facilities over the next few years.