The 193-member UN General Assembly adopted the resolution in a vote of 128 to nine with 35 abstentions.
President Dalia Grybauskaitė's chief foreign policy adviser, Nerijus Aleksiejūnas, said in a comment forwarded by the president's spokeswoman that "Lithuania has consistently held that the issue of Jerusalem can only be resolved through negotiations".
Lithuanian Foreign Minister Linas Linkevičius has decided not to comment on the reasons for the vote, his spokeswoman Rasa Jakilaitienė told BNS.
Before the vote, Trump threatened to cut off funding to countries that would back the resolution condemning his decision to recognize Jerusalem as Israel's capital.
The resolution "affirms that any decisions and actions which purport to have altered the character, status or demographic composition of the Holy City of Jerusalem have no legal effect, are null and void and must be rescinded in compliance with relevant resolutions of the Security Council".
Lithuania voted in solidarity with most EU member states, including Germany, France and Britain. Five EU countries -- Latvia, Poland, the Czech Republic, Croatia and Romania -- abstained.
Lithuania's vote is not in line with its earlier practice of being one of Israel's strongest diplomatic supporters in the EU, mostly due to the history of Lithuanian Jews and Vilnius' efforts to win favour with the United States.
Many other European countries take a tougher stance toward Israel over the expansion of settlements in the occupied West Bank.