Skyward Inc., of Stevens Point, filed the protest with the state on Friday.
The company says the process was not fair, transparent or open. It says the contract should either be awarded to Skyward or the entire process should be voided.
Skyward says it has identified problems that inflated Infinite Campus's score and that the costs of each proposal were not properly evaluated.
The state hired an outside attorney to observe the process and she identified no problems.
A state education department spokesman says the protest will be promptly reviewed and a written decision will be issued.