Oleg Romantsev continued as the coach for the Russian national side in order to oversee their preparations for 2003 FIFA World Cup in South Korea and Japan. In the initial phase, Russia was in Group 1 together with Slovenia, FR Yugoslavia, and Switzerland, Faroe Islands, and Luxembourg. Russia placed first in the direct qualification process, securing the seven victories, two draw and one loss.
Russia was included in Group H together with Belgium, Tunisia, and Japan. In their opening game, Russia achieved a 2-0 victory against Tunisia and then losing their next match against Japan by 1-0, which caused protests to break out in Moscow. In their final game in the match against Belgium, Russia needed a draw to progress to the next round, but they fell 3-2, and were eliminated.
Romantsev was fired immediately following the tournament and replaced by the CSKA's Valery Gazzaev. The job was difficult for him because Russia's squad comprised from Switzerland, Republic of Ireland, Albania, and Georgia with the Irish being considered the favourites, and an improved Swiss team that was becoming a more formidable threat. Russia started their campaign with victories at home in the games against Ireland and Albania however they lost their next two matches away against Albania in addition to Georgia. Gazzaev was dismissed following the draw that was disappointing against Switzerland in Basel and Georgi Yartsev was appointed manager. He was able to be able to qualify Russia for a play-off with Wales following home wins over Switzerland as well as Georgia. In the first play-off match, Russia drew 0-0 with Wales in Moscow however the Vadim Evseev goal brought Russia an 1-0 win in the away match in Cardiff to be qualified for Euro 2004. This victory was marred by the fact that Russian player Yegor Titov was found to be positive for drugs. In the midst of the calls that Russia to be disqualified Titov was handed the ban of one year on February 15th, 2004.
Russia were included in Group A along with host Portugal, Spain, and Greece. They weren't considered to be among the top contenders to make it through and the preparations for the tournament were hampered by injuries to the defenders Sergei Ignashevich and Viktor Onopko. Russia began their tournament with a 2-0 loss to Spain but a last-minute goal by Juan Carlos Valeron put Russia at risk of a elimination in the group stage. The next day, Russia became the first team to be eliminated following an 0-2 loss to Portugal. The final match of the group ended in an unexpected 2-1 win against the eventual champions Greece with Dmitri kirichenko scored one of the fastest goals scored in the tournament.
In 2006's World Cup qualifying tournament, Russia was a part of Group 3 together with Portugal, Slovakia, Estonia, Latvia, Luxembourg, and Liechtenstein. Russia started their qualification by drawing 1-1 against Slovakia on September 4, 2004, in Moscow and later beat Luxembourg with a score of 4-0. However, they suffered a 7-1 loss to Portugal in Lisbon in 2005, which is the most humiliating defeat for Russia. A win over Estonia and Liechtenstein were able to get the team back on track but a draw of 1-1 with Estonia on the 30th of March during Tallinn was a major setback that ended Georgi Yartsev's time in the club. With the new coach Yury Syomin Russia could get back on track with a 2-0 victory over Latvia after a 1-1 draw in Riga on the 17th of August, 2005. Russia was then able to win in the games against Liechtenstein, Luxembourg and a draw 0-0 against Portugal. In their final match, Russia needed to win against Slovakia in Bratislava. After a draw that was 0-0, Slovakia advanced to the play-offs ahead of Russia in goal difference.