Mr Tissainayagam was arrested in March 2008
Sri Lankan President Mahinda Rajapaksa has pardoned a Tamil journalist who received a 20-year prison term on charges of "supporting" terrorism.
Jeyaprakash Tissainayagam had written about the effects of the separatist conflict on the ethnic Tamil minority.
The country's external affairs minister said the pardon had been timed to coincide with World Press Freedom Day.
Mr Tissainayagam's sentence had been criticised by the United States and the European Union.
The president's younger brother and defence secretary, Gotabhaya Rajapakse is openly hostile to the media and has not stopped targeting Sri Lankan and foreign journalists... Whenever a journalist is murdered or kidnapped, he publicly questions the victim's credibility
US President Barack Obama singled out Mr Tissainayagam's case in his World Press Freedom Day address last year as an example of journalists being imprisoned for doing their jobs.
In January, Mr Tissainayagam was freed on bail, pending a full appeal hearing.
He had appealed against his conviction in August last year on charges of raising money for terrorism and causing racial hatred.
Mr Tissainayagam edited the North-Eastern Monthly magazine. He was arrested in March 2008, accused of conspiring to cause ethnic violence through his articles.
The journalist had denied the charges, saying he did not believe in violence.
Mr Tissainayagam's sentence was the harshest given to a Sri Lankan journalist in recent years.
In May 2009 Sri Lanka defeated Tamil Tiger rebels fighting for a separate homeland for the ethnic Tamil minority.
It is estimated that more than 70,000 people were killed during the 26-year conflict.