At a meeting on Tuesday morning, the party's board decided that Pankauskas, 33, should replace Social Democrat Elvinas Jankevičius who resigned from the post last week.
Pankauskas currently serves as an adviser to Prime Minister Algirdas Butkevičius for tourism, youth, migration, investments and non-governmental organizations, the party's deputy leader Gediminas Kirkilas said.
Pankauskas will now be presented to Interior Minister Tomas Žilinskas.
Before his resignation last week, Jankevičius was Lithuania's interior vice-minister from 2013 and was in charge of migration policies, including refugee resettlement.
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