"I met with Tibet's spiritual leader and Nobel Peace Prize Laureate the Dalai Lama, who is visiting our country, for a private conversation in Vilnius," the president posted on her Facebook profile on Wednesday afternoon.
She also posted a photo of the encounter.
Earlier on Wednesday, the president's spokeswoman said she considered such a meeting.
"The possibility of a private meeting between the president and the Tibetan spiritual leader is considered," presidential spokeswoman Daiva Ulbinaitė told BNS on Wednesday.
Lithuanian Foreign Minister Linas Linkevičius had said that since Lithuania stuck to "One China" policy, there would be no official meetings between the Dalai Lama.
The Dalai Lama, 78-year-old laureate of the Nobel Peace Prize, started his third visit in Lithuania on Wednesday afternoon.
During the visit, the 14th Dalai Lama will visit the Lithuanian parliament and Vilnius Town Hall, will deliver a lecture. No official meetings with Lithuania's top leaders have been announced. At the parliament, he will meet with over 40 Lithuanian parliamentarians, as well as the former head-of-state MEP Vytautas Landsbergis, MEPs Leonidas Donskis and Laima Andrikienė.
The Dalai Lama has visited Lithuania in 1991 and 2001. During the last visit, he met with then president Valdas Adamkus for what was described as a "private conversation."
Earlier on Wednesday, activists presented President Dalia Grybauskaitė with a petition signed by over 6,000 people and urging to include the Tibet issue into the European Union's (EU) agenda.
Lithuania is holding the EU Council presidency in the second half of this year.
The official Beijing has accused the Dalai Lama, who fled to India in 1959 after a failed uprising in Tibet against the Chinese rule, of instigating separatism. Meanwhile, the spiritual leader maintains he only wants more autonomy for his homeland in the Himalayas.
In 1989, the Dalai Lama was awarded with the Nobel Peace Prize. He gave up a political post in 2011.