Doncaster council revealed this week that it hoped to rebuild Thorne grammar school as a pound;20 million academy using money from the Vardy Foundation, which was established by multi-millionaire car dealership owner Sir Peter Vardy.
The foundation was criticised last year after reports that another school it funded, Emmanuel College in Gateshead, was teaching creationism.
A Vardy spokeswoman said the organisation was positive about the Doncaster school and stressed it would be open to pupils of all religions, although it would have a "backdrop of Christian values".
The announcement is the latest twist in a public quarrel between the local education authority and Thorne's former head, Tony Brookes, who claims he was put under unfair pressure to resign last year. Dr Brookes said he suspected he was ousted as part of a "master plan" by the authority to make his school an academy.
But Doncaster education director Mark Eales said the head had sent his resignation letter a month before the Government approached the authority about his school's conversion into an academy.
Mr Eales said he had been worried about the performance of Thorne grammar because only a fifth of pupils gained five A* to C grades at GCSE last year and inspectors from the Office for Standards in Education found it had "serious weaknesses" in 2000.
However, Ofsted was forced to apologise to Dr Brookes in December after its independent complaints adjudicator found several problems with the inspection.