"Baku is our first route into Asia and a prime opportunity because of its rapid expansion as a business and tourism centre. There is currently only one other airline operating direct flights between Dubai and Baku so we anticipate strong demand for our service," he said in a statement.
"While the more well-known routes are a mainstay of flydubai's business, it is also our aim to open up the skies and fly to less established locations," he added.
Azerbaijan is bordered by Russia to the north, Georgia to the north-west, Armenia to the west and Iran to the south.
Baku is an ancient trading post with a colourful history including rule by the Persians and Peter the Great.
At the beginning of the 20th Century, the Azerbaijan oilfields produced more than half the world's oil, an accolade only shared in history by the United States.