Turkey's Deputy Prime Minister Bekir Bozdağ flew into Mogadishu to launch the twice-weekly Turkish Airlines service to İstanbul via Sudan's capital Khartoum.
"Somalia was cut off but we have now connected it to the world," he told reporters at Mogadishu's airport on Tuesday.
"We have repaired the airport and now international flights can use it. We have discussed with the president and Turkey will also do local flights inside Somalia."
Somalia has largely been a security vacuum since a dictator was ousted in 1991. Stability is gradually returning to the capital after rebels were forced out by African Union and government troops last year.
Until now, flights into Mogadishu have been operated by small east African operators linking the Horn of Africa nation to neighboring countries.
Turkish Prime Minister Recep Tayyip Erdoğan visited Somalia last August, the first non-African government leader to do so in nearly 20 years.
The Turks have since opened an embassy, improved the international airport, offered Somalis university places in Turkey and made plans to build a new hospital.
Erdoğan's visit reflected Turkey's efforts to boost its profile in Africa, as it has done in the Middle East in recent years, and to promote itself as a model Muslim democracy.
Turkey is behind other emerging countries such as China, Brazil and India in the race for new markets in Africa. But under Erdoğan's Justice and Development Party (AK Party) government, Turkey has boosted trade with the continent and opened several new embassies, particularly in Muslim Africa.