A founder of the National League for Democracy (NLD), he served 19 years in prison for his opposition to military rule in Myanmar, formerly called Burma.
Released in 2008, Win Tin was seen as a close aide to Aung San Suu Kyi but also held the power to disagree with her.
He died in a Yangon hospital early on Monday morning after suffering from health problems.
Win Tin's body lay in state during the afternoon at a cemetery on the outskirts of Yangon.
Aung San Suu Kyi and other activists, political figures and many ordinary citizens filed quietly past.
"Whenever there are clouds above, he will always be our blue sky," one man told AFP news agency.
Freed from Insein prison six years ago, Win Tin continued to wear his blue prison shirt as a protest because others were still being held.
Mourners wore blue prison uniforms as a tribute to him and carried portraits to a memorial service, reports the BBC's Jonah Fisher from Yangon, formerly known as Rangoon.
Much of Win Tin's time in prison was spent in solitary confinement and his sentence was twice extended.
He was known for speaking his mind – not being afraid to criticise members of his own party, in particular those he saw as being too reverential towards Aung San Suu Kyi.
Human Rights Watch executive director Kenneth Roth said Win Tin's death was an "irreplaceable loss" for the South East Asian nation.
"His bravery in the face of cruel hardship continues to echo through Burma's fragile reform process," he said in a statement.
Two years after his release, Myanmar held its first elections in 20 years.
The NLD boycotted the polls but re-entered the political fold as the government embarked on a process of reform that saw some political prisoners freed and media censorship relaxed.
The party now has a small presence in parliament and its key focus is the general election due in 2015.
BBC News, 23 April 2014
Photo caption: Win Tin was Myanmar's longest-serving political prisoner