The last of the daily services operating between the airline's Doha hub and Seychelles International Airport on Mahe Island, will be on August 31.
The decision was taken after careful consideration by the airline's management team.
Qatar Airways Chief Executive Officer Akbar Al Baker said: "I would like to take this opportunity to thank the government of the Republic of Seychelles, the local business and tourism industry, our travel trade partners in the Seychelles and countries around the world for supporting what was a hugely popular destination for Qatar Airways since we launched the route back in 2004.
“Unfortunately we have taken the decision to suspend the route due to commercial reasons which is regretted.
"We have built up a strong relationship with our partners over the years and will continue to work with them and the relevant authorities to ensure a smooth discontinuation of the route. At Qatar Airways, we always remain optimistic and look forward to the day when we can resume operations to these idyllic islands.
"Qatar Airways has informed the travel trade of the decision and all efforts are being made to ensure travel agents, tour operators and individual travellers who have made bookings on the affected route, are re-protected on other airlines or given a full refund.