"According to a directive we issued to the domestic airlines, from now on the airlines will be authorised to take off at least 30 minutes after the morning Azan (the pre-dawn call to prayer)," civil aviation chief Hamid Reza Pahlevani said.
He said the decision was taken "so that passengers can fulfil their religious duty of prayer."
Iran has practised Islamic sharia law since its 1979 Islamic revolution. Iranian carriers do not serve alcoholic beverages nor non-halal food on either domestic or international flights.
On long-haul flights, in-cabin monitors also show the direction of Mecca, to which Muslims turn at prayer.
Pahlevani also reiterated the requirement that all flight crew and ground personnel observe the Islamic dress code.
On Iranian airlines, all air hostesses wear a headscarf and long coat, and air stewards do not wear ties as they are deemed a symbol of Western culture.
All women in Iran beyond the age of puberty, regardless of their nationality or religion, are required to cover their hair and much of the body. Those who do not abide by the dress code risk arrest.