to be in school = to attend school, to go to school to be at school = to be physically at a school taking a class the school = this particular school, "he is the best student in the school"

This can be tricky because there is some overlap in meaning. To say a student attends school regularly, you use, "he is in school" or "he goes to school." He need not physically be in the school at that time or on the way to the school. This describes a regular habit To say a student is physically in school, you can say either "he is at school" or "he is in school". He could be in the school building or on the playground or even at another school activity at another location. This describes a point in time. You need to have the context to determine which use of "in" it is. To distinguish between being on the property of the school, say on the playground, and actually in the school building, you would use, "he is in the school." This describes a point in time and a specific place.