Ghazizadeh Hashemi handed in his resignation to the president in late December.
Rouhani on Thursday accepted it and appointed Saeed Namaki as the caretaker minister.
The president also appreciated Ghazizadeh Hashemi’s efforts over the past six years as health minister.
Reports suggest that a reduction in the health sector budget in the budget bill for the next Iranian calendar year has been the reason behind his resignation.
Namaki previously served as the scientific, cultural, and social deputy of the Plan and Budget Organization.