The 66-year-old lower house Speaker was elected with 403 out of 636 parliamentary votes.
Many NLD MPs are looking to Win Myint to protect farmers’ rights, a controversial issue after decades of land grabs.
The former barrister beat the military candidate and military-appointed acting president Myint Swe while the generals still control three of the most important ministries and are guaranteed a quarter of parliamentary seats.
Suu Kyi’s civilian National League for Democracy (NLD) administration has found itself largely powerless since taking office in 2016.
The military-drafted 2008 constitution gives the generals control of the home, border security and defence ministries, giving them an ongoing grip on domestic and security affairs.
Suu Kyi, 72, is not allowed to take the presidency under the infamous 59(f) clause in the constitution which bans anyone with a foreign spouse or child from becoming head of state.
Her sons are British, as was her late husband.
Khin Zaw Win, director of the Tampadipa Institute, asked whether Win Myint’s loyalty to Suu Kyi was really an asset to the ailing government.
“To those who are asking, he will be forever Aung San Suu Kyi’s henchman,” he said. “I don’t expect much change in the presidency, unless Win Myint puts the country’s interests before Aung San Suu Kyi’s and that of the military.”
But there is hope Win Myint will help weaken the grip of the ageing generals after opposing the military-appointed MPs in the lower house.
Win Myint has reprimanded military MPs who have not prepared enough for parliamentary debates.
He protested with Suu Kyi during the 1988 democracy movement which was crushed by the junta and he was subsequently jailed several times.
Win Myint was a successful parliamentary candidate in the 1990 general election, but the military invalidated the results and he was denied a seat. He was elected in the 2012 by-elections when the NLD re-entered politics and again in the 2015 general election landslide.
The former geologist reportedly could not see his dying son after the military said he must first give up politics.
Born in the Irrawaddy delta in 1951, Win Myint graduated in geology in Yangon but became a lawyer in the 1980s. He was involved with the NLD’s establishment and became a member of the Central Executive Committee in 2010.
Aung San Suu Kyi remains in charge of the National League for Democracy. Picture credit: Asean Economist