Ellesmere's Primary School was built in the 1950s with large parts of the school now around 70 years old and "temporary" buildings still in use after more than 20 years.
Its head, Stuart Roberts, said the work would provide an incredible environment in which children could learn and play.
Mr Roberts said: "We have been working to improve the school buildings and facilities since we became part of North West Academies Trust in 2016. Since then we have bid for Conditions Improvement Funds annually. This is a fund available to academies and free schools for improving the condition of school buildings and infrastructure."
The first £1 million funding was spent on renewing and upgrading the decaying heating and electrical systems, and beginning to refurbish some classrooms.
"The current building work, worth £1.6m, is replacing the roof that has been leaking and patched up repeatedly for years and years, and replacing the three, demountable classrooms and library that have needed upgrading for many years," Mr Roberts said.
"These are being replaced by permanent, brick built class rooms, with much improved environmental credentials such as heating, insulation, ventilation and solar panels.
"There will also be the same facilities as we have installed in all of our recently refurbished classrooms such as kitchen areas and integrated storage to make the most of the available space. "
In July the school was told it had been successful in its most recent funding bid, which will replace the last of the temporary buildings with permanent one.
"This will provide a state of the art Early Years Department for our Nursery and Reception classes. It is the part of the build that I am most excited about, as we have the opportunity to create something that will support and inspire the children of Ellesmere and surrounding areas for many many years to come.
"It will include three large, free flowing classroom spaces with direct access to freshly landscaped and upgraded outside spaces, so that children's learning can continue inside and out, regardless of weather or other physical barriers.
"Finally, we will be completing the projects with a re-landscaping of the outside spaces around school, to ensure that children have access to high quality play equipment, sports specific areas as well as areas for relaxing, reading and quieter play in a beautiful space.
"We are so lucky to have such a large site, with so much already going on, including our swimming pool, two forest school areas, pond and large playing fields. These builds will finally bring the rest of the school buildings and facilities up to our high standards and provide an incredible environment for the children to learn and play in, as well as facilities that can be shared with other community groups and organisations.
"In total, we will have spent more than £3m on improving the school for the local children and local community, and we can't wait until we can show around."
Steve Docking, chief executive officer of NWAT which also runs several schools across Cheshire, said: “We are all very excited by the changes at Ellesmere. Our vision is to create the best possible learning environment for our children, using cutting edge facilities and ideas to bring the best out of them every day. I’m very confident the completed project will be a valuable asset to the whole community.”