Inspectors will ask Muslim girls who wear the hijab to primary school why they wear it.
The reasons that will be given will then be recorded in school reports, amid concerns that some parents force the girls to wear the headscarf.
On Sunday, the chief inspector of schools, Amanda Spielman, announced the move.
She said that schools could be in breach of laws on equality if they only require girls to wear religious garments.
There were also fears that wearing the hijab at such an age could be perceived to be sexualising young girls, as they are typically worn by young women after puberty as a sign of modesty in the presence of men.
Ms Spielman said: “In seeking to address these concerns, inspectors will talk to girls who wear such garments to ascertain why they do so in the school.”
The investigation comes after a survey for The Sunday Times discovered that 18 percent of the 800 primary schools in England include the hijab as part of their uniform policy – most as an optional item.
Earlier research made by the National Secular Society (NSS) discovered that 42 percent of Islamic schools, which includes 27 primary schools, have a uniform policy that are requiring girls to wear a hijab.
The NSS wrote to the education secretary, Justine Greening, to ask that Muslim girls be given “free choices,” adding that forcing the children to wear the hijab is “entirely at odds with this fundamental British value and with wider human rights norms on children’s rights.”
The letter also expressed fears that various non-Islamic schools were “acceding to fundamentalist pressure to incorporate the hijab into their uniform.”