The airline says all its flights are on schedule but its website has gone down.
Iran's second-largest airline, Mahan Air, says it was hit by a cyber attack on Sunday.
The company has been the target of several cyber attacks in the past.
The company said in a statement that "Mahan Air's computer system suffered a new attack. Due to its important position in the country's aviation industry, it has been the target of such attacks many times before.
The statement added that all its flights were on schedule but the company's website went down.
"Our internet security team has been trying to thwart the cyber attack," airline spokesman Amir Hussain Zulanwari told state television.
Mahan Air is the second largest airline in the country after the national airline Iran Air.
The airline is also on the blacklist of Iranian companies that have been subject to US sanctions since 2011.
In addition to the domestic network, the airline operates to many countries in Europe and Asia.
Iran last month accused Israel and the United States of carrying out cyber-attacks on the country's gasoline distribution system, which disrupted fuel supplies across the country.On the other hand, Israel's Internet infrastructure has also come under cyber attack.
The Black Shadow Hacking Group hacked Israel's largest gay or LGBTQ dating site and the website of an insurance firm.
The hacking group has denied any links to Iran, but the attacks on Israeli websites are being seen as a continuation of the years-long secret cyber war between Israel and Iran.
