The team is for Lithuanian players aged 17 or under at the start of a two-year European Under-17 Football Championship cycle, so players appearing for the team can actually be up to 19 years of age. It is considered a feeder team of the Lithuania under-19 and under-21 teams.
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.