The former rector of Moscow's liberal-leaning New Economic School was one of Russia's leading economists and will join the EBRD in 2016 after fulfilling teaching commitments in Paris.
The London-based EBRD, which was founded in 1991, is dominated by former Soviet countries eager to break away from Moscow's economic sway and Guriev will be its first Russian chief economist.
Guriev told AFP in emailed comments that his appointment was "not a surprise but a great honour".
The bank froze new investments in Russia last year as part of the Western sanctions imposed on Moscow over its alleged involvement in the Ukraine conflict.
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Russia condemned the move at the time as politically motivated and in breach of the EBRD's mandate.
Guriev previously worked as an adviser to former president and current Prime Minister Dmitry Medvedev.
He said he fled Moscow out of fear of being prosecuted for helping write a report critical of oil tycoon Mikhail Khodorkovsky's second conviction.
Before he fled Moscow, Guriev was also helping Russia's top opposition leader Alexei Navalny put together an economic programme and he is seen as a support of the anti-corruption firebrand.
When rumours of the EBRD appointment first circulated last month, Russian President Vladimir Putin told his human rights council: "I don't know why he fled. Nobody made any complaints about him.
"I think he didn't flee; it's just that his wife has been working abroad for a long time, he found a job abroad, went there, they pay better there, and that's it," Putin said.
In recent years, Guriev has contributed to the EBRD's transition reports and has been on the chief economist's external advisory panel.