Bashir was among leaders who responded to a call by Turkish President Recep Tayyip Erdogan to attend the meeting after US President Donald Trump outraged the Islamic world with his recognition of Jerusalem as the capital of Israel.
Images showed Bashir warmly greeted by Erdogan and then attending the family photo and summit plenary session in traditional dress.
Sudan's deadly conflict in Darfur broke out in 2003 when ethnic minority groups took up arms against Bashir's Arab-dominated government, which launched a brutal counter-insurgency.
The UN says at least 300,000 people have been killed and more than 2.5 million displaced as a result of the conflict.
Top Sudanese officials including Bashir now claim that the conflict has ended, but the region continues to see regular fighting between numerous ethnic and tribal groups.
Bashir is wanted by the International Criminal Court (ICC) for genocide and war crimes related to the conflict, charges he denies.
Erdogan had while serving as prime minister in November 2009 defended Bashir against the charges, saying "a Muslim could not commit genocide, he is not capable of it".
However Bashir scrapped a plan that month to attend an Organisation of Islamic Cooperation meeting in Turkey after the EU pressured Ankara over his attendance.
Turkey at the time pointed out it is not a signatory to the treaty, which set up the Hague-based ICC.
Wednesday's meeting is the first time that Bashir has visited Turkey since that controversy, and there have been no reports of such pressure concerning his current appearance.
Bashir most recently visited Russia on November 23 where he held talks with President Vladimir Putin.
Iranian President Hassan Rouhani, Jordanian King Abdullah II and Lebanese President Michel Aoun are among the heads of state attending the emergency summit in Istanbul, as well as the emirs of Qatar and Kuwait and presidents of Afghanistan and Indonesia.
A surprise guest was Venezuela's leftist President Nicolas Maduro whose country has no significant Muslim population, but is a bitter critic of US policy.
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