"I see this decision made by the people of Britain as the beginning of a new era for Britain and the EU," Erdogan said during a fast-breaking dinner late on Friday, in his first comments on the shock referendum result.
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"Like the entire world, we expected a 'yes' result in the referendum but it turned out like that," he said.
Voters in Britain decided Thursday to leave the EU, raising questions over the future of the bloc.
London has traditionally been a strong supporter of Ankara's long-stalled bid to join the bloc, but the issue turned into a key theme of Britain's referendum campaign, which was largely focused on immigration.
Erdogan said the problem today "is not Turkey but the EU itself."
He warned that new breakups would be "inevitable" unless the EU renewed its policies toward migrants, rising racism and Islamophobia in Europe.
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"Turkey will naturally take its place within the union if the EU sincerely questions itself and does what's required swiftly," he said.
"If that does not happen and the EU proceeds on its path by deepening its inconsistency, it will be inevitable for (the EU) to face new breakups in a short while."
After applying in 1987, Turkey began EU accession talks in 2005 but its membership bid has been held up by an array of problems, with Erdogan this week suggesting Turkey could hold its own referendum on whether to continue its accession efforts.
On Friday, he blasted the EU's attitude towards Turkey as "Islamophobic".
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"The treatment of Turkey now is Islamophobic. That's why they are delaying taking us in."
Erdogan also criticised British Prime Minister David Cameron who during the referendum campaign said Turkish membership was not "remotely on the cards" and may not happen until the year 3000.
"What did he say? He said 'Turkey cannot join before 3000'," Erdogan said.
"What happened now? Look, you could not stand for even three days" after the vote, he jibed, referring to Cameron's announcement that he would resign by October.
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