"His application was approved," migration office Martin Reichlin, a spokesman for the Federal Migration Office, told AFP.
The one-year residency was granted to the 50-year-old foe of Russian President Vladimir Putin on Thursday and comes with the possibility of renewal.
Khodorkovsky has been living in Switzerland since shortly after he was suddenly pardoned and released from jail in Russia on December 20.
In accordance with complicated Swiss immigration laws, he had to first win approval for settling in a specific canton -- in this case St. Gallen, where his family lives and his children go to school.
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Khodorkovsky, who was once Russia's richest man, is rumoured to still have a fortune of more than 100 million Swiss francs (USD 113 million, 82 million euros), according to the NZZ am Sonntag weekly.
He was an influential politician with presidential ambitions who openly opposed Putin when the former KGB spy first entered the Kremlin in 2000.
Khodorkovsky left Russia immediately after his sudden release and has vowed not to return until the authorities drop old lawsuits against him worth hundreds of millions of dollars.
He has not given up his political activities though.
Earlier this month he visited Kiev and addressed a rally, slamming Moscow's interference in Ukraine.