The content of Ambassador Lina Antanavičienė's meeting with Chinese officials is still withheld.
China has been protesting against meetings between foreign leaders and the Dalai Lama whom it accuses of fuelling violence.
Meanwhile the spiritual leader, who fled to India in 1959 after a failed uprising in Tibet against the Chinese rule, maintains that he seeks more autonomy for his homeland in the Himalayas.
Grybauskaitė met with the 14th Dalai Lama for a "private conversation" in Vilnius on Wednesday evening, her spokeswoman said.
"I hope that you will enjoy meetings with people because people love you. For me it is an honor to able to meet you," Grybauskaitė told the Dalai Lama. Excerpts from the meeting are available on the president's website, president.lt.
In the framework of his third visit in Lithuania, the Tibetan spiritual leader is visiting the Lithuanian parliament on Thursday.