Congratulating U Htin Kyaw, Obama said he "looks forward to working with him and the new government".
"U Htin Kyaw's inauguration represents a historic milestone in the country's transition to a democratically elected, civilian-led government," he said in a statement.
This extraordinary moment in Myanmar's history is a testament to its people, institutions, and leaders who have worked together to ensure a peaceful transfer of power, and it speaks to the significance of the reforms the country has undertaken since 2011, he said.
"The United States looks forward to being a friend and partner of the new government and the people of Burma as they make progress toward building a more inclusive, peaceful, and prosperous future," he said.
The 69-year-old president, a close aide of Aung San Suu Kyi, was today sworn in as president of Myanmar, that entered a new era with the Nobel Laureate's democracy movement assuming power after 50 years of military domination.