Estonia qualified one athlete for the boys event based on its performance at the 2017 World Archery Youth Championships.

[6] Estonia qualified both boys and girls team based on the FIBA U18 3x3 National Federation Ranking.

[7][8][9] Estonia qualified one rhythmic gymnast based on its performance at the European Qualification Event.

[11] Estonia qualified one athlete based on the rankings in the Buenos Aires 2018 Olympic Standings.

[12] Estonia qualified one rower based on its performance at the 2018 European Rowing Junior Championships.