Polling stations opened at 7 a.m. and closed on 8 p.m. A total of 2,487,745 people were eligible to vote.
The runoff sees Ingrida Simonyte, a former finance minister and now a MP nominated by the conservative Homeland Union–Lithuanian Christian Democrats, competing against Gitanas Nauseda, an economist standing as an independent.
Candidates of 16 political parties and public election committees are vying for Lithuania's 11 seats in the European Parliament.
Voter turnout in Lithuania's presidential runoff was 53.43 percent, the Central Electoral Commission said after the polls closed on Sunday.
The turnout rate is lower than in the first round two week ago, but higher than in the second round of voting in the 2014 presidential election.