Ihsanoglu met Monday with Somali President Hassan Sheikh Mohamud and newly appointed Prime Minister Abdi Farah Shirdon Saaid.
Mohamud was elected in September along with some parliamentary leaders. Prior to last month, there hasn't been a formal central government in Mogadishu since the early 1990s.
The OIC, in a statement, said Ihsanoglu's visit, the first for an OIC secretary-general, "conveys a message of support for the new Somali leadership and for stability and peace in this country torn by more than two decades of civil war."
Augustine Mahiga, U.N. special envoy for Somalia, had said in a briefing from Nairobi that Somalia was moving "from transition to transformation."
The Somali government has struggled to maintain control against threats from al-Shabaab, an al-Qaida affiliate in control of parts of the country.
Kenyan and pro-government forces captured the port city of Kismayo, one of the last strongholds of al-Shabaab in Somalia. Mahiga warned that the declining influence of al-Shabaab didn't mean the threat was eliminated, however.