These five Airbus A380s, which have two floors and, in some configurations, can carry 615 passengers, took off on Tuesday morning.
The aircraft's destinations are Jeddah, Manchester, Paris, London and Frankfurt.
On Monday, the first flights took off from Dubai and Abu Dhabi in the United Arab Emirates, after the US and Israel's attack on Iran - and Iran's response with its own attacks in the region - closed airspace and disrupted air traffic.
Emirates urges travelers not to go to the airport unless they have received notification that they have been rebooked.
Qatar Airways, the Doha-based airline, wrote on X that the airspace over Qatar remains closed, and promised an update only on Wednesday.
