Ground works were held-up when the slow worm colony was discovered at Oldfield Primary School in Maidenhead.
But ecologists have now moved them to safety allowing Leadbitter to start on site this week.
The new school is now due to be completed by September 2015.
Richard Jarrett, headteacher at Oldfield, said: “All the staff and children are excited that the work has finally started and our new school will soon start to take shape.
“We have involved the children in the process – including learning a little about the slow worms – and look forward to the pupils playing a key part in the grand opening next year.”