The knockout stage began with the quarter-finals on 24 June and ended with the final on 4 July 2004 at the Estádio da Luz in Lisbon.
Greece won the tournament with a 1–0 victory over the host nation Portugal.
For the first time in an international football tournament, the silver goal system was applied, whereby the team who leads the game at the half-time break during the extra time period would be declared the winner.
The top two placed teams from each of the four groups qualified for the knockout stage.
Man of the Match: Ricardo Carvalho (Portugal)[1] Assistant referees: Rudolf Käppeli (Switzerland) Francesco Buragina (Switzerland) Fourth official: Alain Hamer (Luxembourg) Man of the Match: Angelos Charisteas (Greece)[2] Assistant referees: Kenneth Petersson (Sweden) Peter Ekström (Sweden) Fourth official: Stuart Dougal (Scotland) Man of the Match: Ruud van Nistelrooy (Netherlands)[3] Assistant referees: Igor Šramka (Slovakia) Martin Balko (Slovakia) Fourth official: Markus Merk (Germany) Man of the Match: Milan Baroš (Czech Republic)[4] Assistant referees: Vladimir Eniutin (Russia) Yuri Dupanov (Belarus) Fourth official: Urs Meier (Switzerland) Man of the Match: Luís Figo (Portugal)[5] Assistant referees: Kenneth Petersson (Sweden) Peter Ekström (Sweden) Fourth official: Ľuboš Micheľ (Slovakia) Man of the Match: Traianos Dellas (Greece)[6] Assistant referees: Marco Ivaldi (Italy) Narciso Pisacreta (Italy) Fourth official: Valentin Ivanov (Russia) Man of the Match: Theodoros Zagorakis (Greece)[7] Assistant referees:[8] Christian Schräer (Germany) Jan-Hendrik Salver (Germany) Fourth official: Anders Frisk (Sweden)