The cause of the fire is not yet known, with investigations continuing. The country's anti-terrorism chief Boniface Mwaniki has said he does not believe the fire was connected to terrorism, however.
No serious injuries were reported.
The fire started in the airport's international arrivals and immigration area at 05:00 local time and spread quickly.
The Kenya Airports Authority (KAA) diverted inbound flights to Mombasa and Eldoret.
JKIA is East Africa's biggest airport serving more than 15,000 passengers daily and its closure – described as a "major disaster" – caused widespread disruption.
A plane from London was the first to land at 06:30 this morning.
Fly540 Kenya, East Africa's premier low cost airline, resumed flights yesterday evening with two Fly540 Kenya flights departing JKIA for Mombasa and Kisumu. It is intended that 11 flights will take place today to Eldoret, Juba, Kisumu, Lamu, Lodwar, Malindi, Mombasa and Zanzibar.
Don Smith, CEO of Fly540 Kenya, said: "We thank the Kenyan Aviation Authority for their efforts to get the aircrafts back in the air as quickly as possible. Talks of prolonged disruptions and diversions to other airports were premature, and we are pleased that we are able to commence a fuller service today. We appreciate the patience shown by our passengers during this time of great inconvenience. All of our staff are working hard towards normalising operations as quickly as possible."
Image: © KAA
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