Flights have been operational again since 11:00 pm (1930 GMT) Sunday and were being "carried out in accordance with the flight schedule", said Jafar Yazarloo, spokesman for Iran's Civil Aviation Organisation, quoted by the IRNA state news agency.
Iran on Tuesday launched around 200 missiles in its second direct attack on Israel, in what it said was retaliation for the killing of Tehran-aligned militant leaders in the region, along with a general in Iran's Revolutionary Guards.
Ever since, Israel has said that it will respond to Iran's attack.
Iran initially closed its airspace for less than two days, from Tuesday night until Thursday morning.
The aviation body announced then that both domestic and international flights were grounded for security reasons until the reopening.
The European Union Aviation Safety Agency has advised European airlines to avoid Iranian airspace until October 31, with the situation under ongoing review.
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