He beat MP Artūras Paulauskas in the race for the post.
In a secret ballot in the country's central city of Kėdainiai, Mazuronis was supported by 613 participants of the party's congress, while Paulauskas collected 264 votes.
Mazuronis, the new leader, said his primary task was to build a strong team.
"Secondly, (we have to) become more active in the position where we have delegated ministers and elected people. We have to work out a serious program for down-to-earth people who understand hopes and expectations of ordinary people," Mazuronis told journalists after the election.
He said he had no plans of giving up his MEP mandate until the parliamentary elections scheduled for next year.
"Until the Seimas elections, I will work both at the European Parliament and Lithuania. If voters have confidence in our team, if they want to have the same, let's say, environment minister, and vote for us, I will come back," said the new leader of the Labor Party.
Speaking about the Labor Party's bookkeeping fraud case currently heard at the Court of Appeals, Mazuronis said political and judicial processes should be separated.
Mazuronis, 61, was a member of Lithuania's parliament for many years and headed the Environment Ministry before being elected to the European Parliament in 2014. He is a member of the Alliance of Liberals and Democrats for Europe (ALDE) there.
He will now replace Parliamentary Speaker Loreta Graužinienė who stepped down from the Labour Party's leadership in March following the unsuccessful local elections.
Established in October of 2003, the Labour Party currently has 29 mandates in Lithuania's 141-seat parliament.
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