Dr Than Htut Aung "continued to pursue a critical editorial line, risking censorship, jail, torture, or worse" during the years of dictatorship, Erik Bjerager, president of the World Editors Forum, said when handing over the award in Bangkok today.
Dr Than Htut Aung, who founded the Eleven Media Group 13 years ago, was briefly arrested in 2003. More recently, in 2011, publishing was suspended for two weeks following the release of Aung Sang Suu Kyi.
Bjerager called it one of the publisher's "boldest, most recognised exploits". He explained that "a front-page headline appeared in which some letters were printed in a lighter shade to spell out: 'Su free. Unite and advance to grab the hope'".
"The publisher has faced heavy government pressure in the past, he faced heavy government pressure and the ever-present censor’s pen. Nonetheless, he consistently defied restrictions on freedom of expression," Bjerager explained to the thousands of people gathered in Bangkok.
With the recent shift to democracy journalists in Myanmar are "rediscovering freedoms after nearly 50 years of censorship and official control", Bjerager added.
"For the media the changes have been dramatic," he said, "with the reappearance in kiosks of private daily newspapers after an absence of 50 years".
But while the speed of reform has been dramatic, the challenges are great, he explained.
Accepting the award at the WAN-IFRA conference in Bangkok, Dr Than Htut Aung said that since he was born he has lived under dictatorship. "But now freedom is in front of me".
Journalism.co.uk is in Bangkok for the World Editors Forum. Follow @SarahMarshall3, @JohnCThompson and #editors13 for updates.