Myanmar's lawmakers Tuesday elected a close aide and longtime friend of Aung San Suu Kyi to become the country's first civilian president in decades, a historic moment for the formerly junta-run nation.

Htin Kyaw, 69, won 360 of 652 votes cast by Myanmar's two legislative chambers, paving the way for him to serve as a proxy for the Nobel laureate who is constitutionally barred from becoming president.

MPs erupted into applause after Htin Kyaw's victory was announced following a lengthy ballot count by hand in the capital Naypyidaw.

‘I hearby declare that U Htin Kyaw has been elected the president with the most votes,’ parliamentary speaker Mann Win Khaing Than told legislators.

Myanmar is in the grip of a stunning transformation from an isolated and repressed pariah state to a rapidly opening aspiring democracy.

In November, Suu Kyi's National League for Democracy won a thumping victory at the polls, allowing her party to dominate Myanmar's two legislative houses.

But the military remains a powerful force in the Southeast Asian nation and has refused to change a clause in the junta-era constitution that bars Suu Kyi from top political office.

The veteran activist has instead vowed to rule ‘above’ the next leader.

Her choice of Htin Kyaw to act in her place is seen as a testament to her absolute faith in his loyalty.

Myanmar's new president will replace incumbent Thein Sein at the end of the month following five years of army-backed quasi-civilian leadership that has been lauded for steering the nation out from the shadow of outright military rule.

The two other candidates who were also running in Tuesday's will now become the country's joint vice presidents.

They are retired general Myint Swe, an army-backed candidate who remains on Washington's sanctions list and won 213 votes, and ethnic Chin MP Henry Van Thio, who gathered 79 votes.

Most of Myint Swe's votes came from the army's parliamentary bloc, which is reserved a quarter of seats in parliament, and from military-backed parties.

- Many challenges -

Suu Kyi, 70, has unrivalled popularity both as the daughter of the country's independence hero and as a central figure in the decades-long democracy struggle.

Her party's huge election victory was seen as a further endorsement of her political star power, as millions were swept to polling stations by the NLD's simple message of change.

Months of negotiations with army chief Min Aung Hlaing have failed to remove the obstacles blocking her from power.

Suu Kyi is barred from the presidency by a clause in the charter because she married and had children with a foreigner.

It is not yet clear what role she plans to take or how she will manage the relationship with the country's new president.

A new cabinet, set to be announced at the end of the month, is expected to include figures from across the political spectrum as Suu Kyi looks to promote national reconciliation.

It will swiftly set about facing the country's many challenges, including poverty, civil wars in ethnic minority borderlands and decrepit infrastructure.

Senior party figures say one of the government's first tasks will be to whittle down myriad ministries by combining overlapping portfolios. 

While little known outside Myanmar, Htin Kyaw, who helps run her charitable foundation, commands considerable respect inside the country, partly because his father was a legendary writer and early member of the NLD.

He is married to sitting NLD MP Su Su Lwin, whose late father was the party's respected spokesman.

The military's choice of Myint Swe, seen as a hardliner and close ally of former junta leader Than Shwe, however is proving controversial in a nation still smarting from half a century of army dominance.