Mr Obama told the Dalai Lama of his “strong support” for human rights in Tibet, a White House statement said.
Beijing released an angry statement saying the meeting had damaged relations between the two countries.
Mr Obama’s last meeting with the Dalai Lama in February 2010 also drew strong condemnation from Beijing.
The talks – which lasted about 45 minutes – were held in the Map Room rather than the Oval Office, which is traditionally reserved for visiting heads of state.
“The president reiterated his strong support for the preservation of the unique religious, cultural and linguistic traditions of Tibet and the Tibetan people throughout the world,” the White House statement said.
“He underscored the importance of the protection of human rights of Tibetans in China.”
Mr Obama also reiterated that the US considers Tibet to be part of China, and said that he encouraged “direct dialogue to resolve long-standing differences”.
The closed-door meeting came just hours before the Dalai Lama was scheduled to leave Washington at the end of an 11-day Buddhist ritual.
China had earlier warned the US not to receive the Dalai Lama.
“Such an act has grossly interfered in China’s internal affairs, hurt the feelings of Chinese people and damaged the Sino-American relations,” Chinese Foreign Ministry spokesman Ma Zhaoxu said in a written statement following the meeting.
“We demand the US side to seriously consider China’s stance, immediately adopt measures to wipe out the baneful impact, stop interfering in China’s internal affairs and cease to connive and support anti-China separatist forces that seek ‘Tibet independence’,” Mr Ma said.
The White House has not commented on Beijing’s displeasure.
The Chinese authorities have long vilified the Dalai Lama as a “splittist”, although he has repeatedly stated that his goal is for meaningful Tibetan autonomy rather than independence. – BBC news