An approximate cost estimate is between USD500 and USD1250. It depends entirely on the features, functionality and quality. For a more accurate estimation, we need to see a complete list of functionality. If the system is intended to be used for accepting offline payments alongside online, the estimate is likely to go higher.
As per my understanding, several types of school officials such as admin, principal, accountant etc. will be simultaneously working on it. There should be a registration interface both for the student and guardians. The fee structure is also an important matter of consideration. All fees need to be pre-determined by the admin. It is not possible to make a final estimate without studying the key features.