Emin Huseynov flew out of Azerbaijan on the plane of Switzerland's top diplomat Didier Burkhalter, who attended the Euro Games ceremony in Baku late on Friday, the federal department of foreign affairs said.
His departure came after months of negotiations with the Azerbaijani authorities, department spokesman Jean-Marc Crevoisier told the ATS news agency.
The 35-year-old journalist and rights activist was currently in Bern, did not for the moment wish to speak to the media and has until September to decide whether he wants to apply for asylum in Switzerland, Crevoisier was quoted as saying.
A fierce critic of authoritarian President Ilham Aliyev's human rights record, Huseynov has been sheltering at the Swiss embassy in Baku since August 18th 2014 when he evaded Azerbaijani police to enter the building posing as a Swiss national.
At the time, the activist had been sought by prosecutors on charges of “illegal entrepreneurship and tax evasion.”
Switzerland allowed him to remain at its embassy for “humanitarian reasons.” Energy-rich Azerbaijan has pumped vast resources into hosting the first edition of the European Games sporting extravaganza billed as Europe's answer to the Olympics from June 12th-28th, building state-of-the-art facilities in a bid to burnish its image.
But international and local rights activists have been using coverage of the glitzy event to draw the world's attention to the widespread human rights abuses in the Caucasus country.
Human rights groups accuse Aliyev's government of consistently using spurious charges to jail regime critics and of stepping up a campaign to stifle opposition since his election for a third term in 2013.
Aliyev, 53, came to power in 2003 following an election seen as flawed by international observers.
He took over after the death of his father Heydar Aliyev, a former KGB officer and communist-era leader who had ruled newly independent Azerbaijan with an iron fist since 1993.