Zapolskas would replace Agila Barzdienė, who plans to take on a new role in civil service.
"The expertise of Zapolskas, highly experienced diplomat, will be very important not only for further successful operations of the institution, but also for preparations for Lithuania’s presidency over the EU Council in 2027," Nausėda is cited as saying in a press release from his office.
Zapolskas, former ambassador to Sweden, Italy and the Vatican, had headed the Foreign Ministry’s State and Diplomatic Protocol Department since 2022.
He is expected to take office on 2 January.