"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 20th.
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.
Even though Khodorkovsky is not planning on working in Switzerland -- often a prerequisite for gaining residency -- a permit can be given when it is "in the public interest," Reichlin said.
The canton had justified its decision with the substantial tax revenue it expects to gain from the Russian's residency, he added.
Khodorkovsky, who was once Russia's richest man, is rumoured to still have a fortune of more than 100 million francs ($113 million), 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's arrest in 2003 and subsequent convictions on fraud and embezzlement charges have been widely condemned by Kremlin critics as an effort by Putin to silence his most potent rival.
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.