Polling stations in 68 single-member constituencies around the country are opening at 7 a.m. and closing at 8 p.m. Voters are asked to wear facemasks and bring their own pens as part of coronavirus precautions.
Results are expected at around midnight.
"We expect to have the results much earlier (than in the first round), possibly at midnight," Laura Matjosaityte, head of Lithuania's Central Electoral Commission, has told BNS.
Seventy of 141 members of the Seimas were elected in the nationwide multi-member constituency in the first round on October 11.
Since only three candidates secured an outright victory in their single-member constituencies two weeks ago, the two front-runners in the remaining 68 constituencies are competing for seats in the runoff.
The new parliament usually holds its first sitting in mid-November.