The proposals for the world heritage site will create a £25 million visitor centre at Airman's Corner with enhanced exhibition and education facilities. Transport improvements include closing and grassing over a section of the A344 that runs close to the stones and removal of the car park.
A transit system taking people from the visitor centre to the stones site is also proposed along with upgrading the Airman's Corner junction to a roundabout.
The scheme has been put together with help from the National Trust and the South West Regional Development Agency. It is significantly cheaper than previous plans that entailed running the A303 through a tunnel, estimated to cost £500 million.
English Heritage is set to unveil the visitor centre designs next week. After registering the application, Wiltshire Council will carry out a public consultation.