The team is for Lithuanian players aged 17 or under at the start of a two-year UEFA European Under-17 Championship cycle, so players appearing for the team can actually be up to 19 years of age.

Prior to Lithuania's independence in 1991, Lithuanian players were eligible for selection to the Soviet Union U-16 team.

Following the dissolution of the Soviet Union, the Lithuanian Football Federation was admitted to UEFA as a full member in 1992, and the Lithuania U-16 team played their first competitive matches in the first phase of the qualifying tournament for the 1994 European U-16 Championship.

The team's competitive debut came on 30 August 1993 against Wales U-16 and they finished their first qualifying campaign as 3rd out of 3 teams, behind Wales and Iceland.

The following players were called up for the 2025 UEFA European Under-17 Championship qualification matches on 29 October - 4 November 2024.