The move is designed to gather more information on the practice, which was outlawed in the UK in 1985, and to help women at risk.
It comes ahead of the United Nations' Day of Zero Tolerance to FGM on Thursday.
At least 66,000 girls and women in the UK are believed to be victims.
The Department of Health says from April, all NHS hospitals will be able to record if a patient has undergone FGM or if there is a family history of this.
By September, all acute hospitals will have to report this data to the Department of Health, on a monthly basis.
The government says this is the first stage of a wider scheme to improve the way the NHS will "respond to, follow up and support the prevention of FGM".
It is hoped this will, in the autumn, provide the first snapshot of how many women have been treated by the NHS for FGM, and in the longer term, help identify families where girls might be at risk.