Erdoğan, accompanied by his family and five cabinet ministers, has in the past days appealed for more food aid for the drought-hit nation and lashed out at wealthy Western nations for not doing more.
Somalia's President Sheikh Sharif Ahmed welcomed Erdoğan at the airport with a warm embrace, before Turkey's premier, dressed in a sharp, crisp suit and his wife in haute-couture Islamic dress drove through the city's rubbish-strewn streets.
At one dusty, windswept refugee settlement, Erdoğan crouched inside the tent of Bashir and Fatima, a young couple mourning the loss of two of their four children who died after trekking 90 km (55 miles) to Mogadishu.
Erdoğan's wife Emine handed out chocolates and sweets.
The Organization of the Islamic Cooperation (OIC) countries pledged on Wednesday $350 million in aid to fight the famine which has left 3.7 million Somalis at risk of dying of hunger.
Erdoğan has said he hoped the OIC's efforts would jolt the consciences of those ignoring the unravelling humanitarian emergency.
The withdrawal of most Islamist militants from their Mogadishu bases earlier in the month has effectively handed full control of the capital to the government for the first time since civil war broke out in 1991.
MOMENTOUS VISIT
Somali troops and African peacekeepers are, though, still meeting pockets of rebel resistance in the city, highlighting the view of regional observers that the al Qaeda-linked al Shabaab insurgents are far from defeated.
Security forces flooded Mogadishu's main streets where Turkish flags fluttered in the coastal breeze and posters adorned the walls of mortar-blasted buildings.
"Prime Minister Erdoğan's visit tells us the Turkish people are closer to us than any other Muslim nation on earth," said resident Abdirashid Ali Omar. "The Turkish people are here to share with us in our time of need. It is momentous."
The U.N.'s World Food Programme said on Friday it was still unable to reach 2.2 million hungry people living in areas of southern Somalia controlled by al Shabaab, whose bloody campaign to topple the government has cost more than 20,000 lives.
Aid agencies say that while droughts are a natural phenomenon, this famine is largely down to conflict and bad governance.
"Droughts will happen. They always will, but they don't have to be disasters. They can be managed," Oxfam's Philippa Crosland-Taylor said in neighbouring Kenya.