Thein Sein became the first head of Myanmar to visit the White House in 47 years, and he and Obama sat down for talks in the Oval Office.
Obama said the Myanmar leader had assured him that he intends to move forward on releasing more political prisoners and institutionalizing political reforms that have already taken place. Thein Sein also vowed to resolve ethnic conflicts by incorporating all communities into the political process, Obama said.
"I also shared with President Sein our deep concern about communal violence that has been directed at Muslim communities inside Myanmar. The displacement of people, the violence directed towards them needs to stop," Obama said.
Sein, speaking through a translator, said his country faces a "daunting task" in carrying out reforms but said for democracy to flourish in Myanmar the reforms must be carried out in the years ahead.
Myanmar will need the "assistance and understanding" of the international community, including the United States, as it goes through the process, he said.
Rights groups and some US lawmakers fear Obama has moved too quickly since forging a dramatic breakthrough in relations in 2011 after half a century of military rule in Myanmar, also known as Burma.
US officials argue that reforms by Myanmar's quasi-military government - freeing democracy activist Aung San Suu Kyi and hundreds of political prisoners, scrapping censorship, legalizing trade unions and protests - are transformative and deserve support from Obama, who confirmed the end of Myanmar's pariah status with the West with a landmark visit last November.
However, ethnic or sectarian violence, particularly in the western state of Rakhine, has worsened since Washington started easing sanctions, and a Reuters special report published last week found apartheid-like policies segregating minority Muslims in prison-like ghettos there.
At least 192 people died last year in violence between Buddhists in Rakhine and Rohingya Muslims, who are denied citizenship by Myanmar. Most of the victims, and the 140,000 people made homeless in the attacks, were Muslims.