He is first top US diplomat ever to visit Somalia.
Kerry arrived at Mogadishu's airport shortly before noon local time, greeted by Somalia's president and prime minister on the tarmac. He immediately entered a series of planned meetings that include both of them along with regional leaders and civil society groups.
"I'm glad to be here," Kerry said.
"This is a great moment for us. Thank you for the time to be with us," President Hassan Sheikh Mohamud said as they sat down together.
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And the fact that he was only dipping his toe in Somalia, and not venturing past the airport, highlighted just how dangerous and instable the country remains.
"The next time I come, we have to be able to just walk downtown," Kerry told Somalia's president. Mohamud replied, downtown "is very different now."
Top of the agenda is the fight against al-Shabab. African forces and US drone strikes have crippled the organisation's leadership in recent years and left the extremists without much of the territory they once controlled or the cash flows needed to reverse their losses.
Last month's massacre at Kenya's Garissa University College killed 148 people, mostly students, and underscored the group's capacity to carry out relatively unsophisticated but extremely deadly terrorist attacks far from its bases of operations.
Kerry's trip is designed "to reinforce the United States' commitment to supporting Somalia's ongoing transition to a peaceful democracy," spokeswoman Marie Harf said in a statement.
"He will discuss security cooperation and Somalia's progress towards meeting its reform and development benchmarks," she said. "He will also meet with civil society leaders to discuss the importance of a vibrant NGO sector and thank African Union troops for their role in stabilising Somalia."
Militias, Islamist extremist groups and Somalia's nominally national military all vied for power before the tide turned against al-Shabab earlier this decade. Piracy also has been a major problem.