Mr Kim was chosen by Interpol's 194 member states at a meeting of its annual congress in Dubai.
He beat Russia's Alexander Prokopchuk, who had been widely tipped to win.
But there was growing concern that Mr Prokopchuk would use the role to target critics of Russia's President Putin.
Moscow said Mr Prokopchuk would continue to serve as an Interpol vice-president and help strengthen the organisation's "position in the international police community". On Tuesday, it hit back at what it called a "campaign aimed at discrediting" the Russian candidate.
The election follows the disappearance of Interpol's former president Meng Hongwei, who vanished on a trip to China in September. Beijing has since confirmed he has been detained and is being investigated for allegedly taking bribes.
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