Ilya Barabanov, 24, works at Novoye Vremya (The New Times), an independent Moscow weekly which came under fire from the government after publishing an article reporting on alleged abuses by "an elite police subdivision directly under the interior minister", according to an announcement by the awards.
This reportedly prompted a search of the New Times' editorial offices and a lawsuit being filed against the publication, which Barabanov is said to have publically condemned as a violation of media law.
The award, which is administered by the US branch of Reporters Without Borders and the Global Media Forum, aims to recognise journalists and editors who fight ethically to report the news in countries where there are restrictions on the press.
It was set up last year in memory of Peter Mackler, a former chief editor for North America at Agence France-Presse who died of a heart attack in June 2008.
According to a blog post by the awards site, Jean-François Julliard, secretary general of Reporters Without Borders, said Barabanov's courage is "essential" for the future of journalism in Russia.
"We are delighted to know this award goes to Ilya Barabanov", he said. "Being a journalist in Russia is one of the toughest jobs around. Russian journalists need to be supported and recognized worldwide for the work they do. Ilya's talent, courage and persistence are essential to Russian journalism."
According to AFP Barabanov will receive his award at a ceremony in October where the first winner, JS Tissainayagam, a Sri Lankan reporter accused of supporting terrorism is also scheduled to speak after it was announced he would be pardoned from his 20 year prison sentence.
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