Estonia competed at the 2004 Summer Olympics in Athens, Greece, from 13 to 29 August 2004. This was the nation's ninth appearance at the Summer Olympics.
The Estonian Olympic Committee sent a total of 42 athletes, 31 men and 11 women, competing only in 11 different sports. Sixteen athletes had competed in Sydney, including three Olympic medalists: decathlon champion Erki Nool, and judoka and bronze medalists Aleksei Budõlin and Indrek Pertelson. Rower Jüri Jaanson participated in his fifth Olympics under two different banners (the other one with the Soviet Union) as the most experienced member of the contingent. Discus thrower Eha Rünne, aged 41, was the oldest athlete of the team, while long-distance freestyle swimmer Jelena Petrova was the youngest at age 15. Claiming the nation's first ever gold medal in athletics, Nool was appointed by the Estonian Olympic Committee to become the nation's flag bearer in the opening ceremony.
Estonia left Athens with the same number of medals (3) collected from the previous games, but failed to earn a single gold. After finishing farther from the podium in four consecutive Olympics, Jaanson ended his medal drought by taking home the silver in the men's single sculls. Two bronze medals were awarded to discus thrower Aleksander Tammert and heavyweight judoka Indrek Pertelson, who managed to repeat it from Sydney.
Estonian athletes have so far achieved qualifying standards in the following athletics events (up to a maximum of 3 athletes in each event at the 'A' Standard, and 1 at the 'B' Standard).
Estonia has qualified two judoka
<small>Qualification Legend: FA=Final A (medal); FB=Final B (non-medal); FC=Final C (non-medal); FD=Final D (non-medal); FE=Final E (non-medal); FF=Final F (non-medal); SA/B=Semifinals A/B; SC/D=Semifinals C/D; SE/F=Semifinals E/F; R=Repechage</small>
<small>M = Medal race; OCS = On course side of the starting line; DSQ = Disqualified; DNF = Did not finish; DNS= Did not start; RDG = Redress given</small>
Estonian swimmers earned qualifying standards in the following events (up to a maximum of 2 swimmers in each event at the A-standard time, and 1 at the B-standard time):
Estonia's first appearance in the Olympic triathlon resulted in a twenty-first-place finish for the nation's sole competitor in the sport.