The budget airline's first destinations will be Beirut, Lebanon, starting June 1 and Amman, Jordan, flying on June 2.
Flydubai will operate two next-generation Boeing 737-800 aircraft on the routes, Sheikh Ahmed bin Saeed al-Maktoum, President of the Dubai Civil Aviation Authority, told reporters.
Fares from Dubai to Beirut are selling for about £50 (250 United Arab Emirates Dirham) one-way including taxes.
In addition to owning the largest carrier in the Middle East, Dubai also owns the busiest airport in the region. Dubai International Airport served more than 37 million passengers last year.