Parents gathered to protest outside Batley Grammar School over two days last week, after a teacher is alleged to have used a "totally inappropriate resource" during the RE lesson.
Headteacher Gary Kibble confirmed the teacher in question had been suspended and said an "independent formal investigation" would take place.
Batley Multi Academy Trust confirmed on Tuesday that the investigation will start on April 12, with an outcome expected towards the end of May.
In a statement, the Trust said: "We‘re grateful for the constructive engagement with all our stakeholders over the last few days.
"We believe the right way forward is for an independent investigation to review the context in which the materials (which caused offence) were used, and to make recommendations in relation to the Religious Studies curriculum so that the appropriate lessons can be learned and action taken, where necessary.
"We understand everyone will want clarity as soon as possible, so can confirm we expect to be able to announce that we have appointed an independent investigation panel over the next two weeks with the investigation commencing on April 12, and anticipate the investigation outcomes towards the end of May."
Officers from West Yorkshire Police attended the protests outside the school in Carlinghow Hill on Thursday and Friday last week. No arrests were made and no fines were handed out.