Mazen Darwish was the director of the Syrian Center for Media and Freedom of Expression when he was arrested in February 2012 in a Damascus security raid, along with two of his colleagues.
The organisation confirmed his release today but said he is still standing trial and is scheduled to attend a court hearing on August 30.
"After an arbitrary arrest that lasted three years, five months, and 23 days, Mazen Darwish has released from prison today," the group said in a statement.
He was one of the rare journalists who dared publish details of arbitrary arrests and violations by policy and security forces.
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He has been standing trial on charges of "publicising terrorist acts."
What began as an Arab Spring-style uprising against Assad's rule became a full-blown civil war in Syria. The conflict, now in its fifth year, has killed at least 250,000 people and wounded more than a million, according to the UN.
International human rights and press freedoms organisations, including the New York-based Committee to Protect Journalists and Amnesty International have long called on the Syrian government to release Darwish. The UN also called for his release.