The move by the NLD will seriously undermine the credibility of any polling in the eyes of foreign governments, which have urged the ruling generals to ensure all groups take part in the elections.
Under rules enacted this month by the military government, which also bar Suu Kyi from participating in the polls, any party that does not register will cease to exist.
Security was heightened, with plainclothes police and pro-government security guards stationed around the party's compound as the delegates met.
Dozens of rank-and-file members of the party gathered outside, some wearing white tops bearing the slogan: "We believe Aung San Suu Kyi".
"We have sacrificed our life for 20 years and finally we have to give up like this. So you can imagine how we feel in our hearts," Nann Khin Htwe Mying, a senior NLD member, said.
Win Tin, a veteran party member and one of Myanmar's longest-serving political prisoners, having spent 19 years behind bars before his release in 2008 was not in favour of keeping the party away from the election process.
"This meeting is a life-or-death issue. If we do not register, we will not have a party and we will be without legs and limbs," he said before the decision.
Win said the journey ahead would be difficult if the party chooses to opt out of elections but that its members could still maintain their democratic principles and spirit.
Last week, Suu Kyi was quoted by her lawyer as saying she opposed registering her party because the government's restrictions on the vote were "unjust". However, she stressed she would let the party decide for itself.
The party won the last election held in Myanmar in 1990 by a landslide but was barred by the military from taking power. The election law brought in by the generals officially nullifies that result.
Suu Kyi is under house arrest and the new election laws effectively bar her from running and voting. One law also instructs political parties to expel members convicted of crimes or face deregistration.
Although the Nobel Peace laureate has been under detention for 14 of the last 20 years, she is still general-secretary of the party and a dominant figure.
The United States has led international criticism of the new election laws, saying they makes a "mockery" of democracy.
Critics have dismissed the poll, planned for November or December, as a sham designed to entrench the power of the military, which has ruled since 1962.