Ramūnas Karbauskis, leader of the Lithuanian Farmers and Greens Union (LVŽS), won a confidence vote in his party's council on Monday evening.
In a secret ballot, the confidence motion was passed with 65 votes in favour, 11 against, one abstention and one vote invalidated, Dalia Vencevičienė, Karbauskis' spokeswoman, said.
Karbauskis had promised to submit his leadership to a confidence vote following three elections earlier this year.
Prime Minister Saulius Skvernelis, the LVŽS candidate in May's presidential election, finished third and failed to advance to the runoff.
The party, which is the biggest in the current parliament, also finished third in the municipal and European Parliament elections .
Karbauskis had vowed to win all three elections and pledged to step down in case of a failure.