Before his trip, Obama insisted the visit was "not an endorsement of the Burmese government."
"This is an acknowledgment that there is a process under way inside that country that even a year and a half, two years ago, nobody foresaw," Obama told reporters in Thailand on Sunday, the first stop on his Asia trip. He added that the country was moving "in a better direction."
Western governments have responded to Myanmar's progressive efforts by easing sanctions that targeted the military regime. On Friday, the U.S. eased restrictions on imports of most goods from Burma.
But the country has also witnessed bouts of turmoil in recent months. Violence between Rohingya Muslims and local Buddhists broke out in the western state of Rakhine.
During the latest eruption of tensions, the United Nations said at least 89 people were killed over two weeks of violence and 110,000 were displaced.
Obama urged Myanmar to use its "diversity as a strength, not a weakness."
"I believe deeply that this country can transcend its differences, and that every human being within these borders is a part of your nation's story."
He met briefly with representatives of civil society organizations, including an advocate for Burma's Rohingya population.
However, some aid organizations questioned whether now is the right time for Obama to add legitimacy to Thein Sein's government.
Burmese exile leaders and human rights advocates have expressed concerns that the visit is too soon, and may not yield the additional reforms that a presidential visit can deliver if it happens at the right time.