Ekimov started training as a cyclist at age 12 with a bicycle school affiliated with the famous centre of Aleksandr Kuznetsov. He trained in Leningrad at Lokomotiv and later Armed Forces sports society during the Soviet era. Ekimov won three Olympic gold medals: in the track team pursuit in Seoul for the USSR, and in an upset, in the roadtime trial in Sydney for Russia. At the 2004 Summer Olympics in Athens, Ekimov won the silver medal for Russia in the men's road individual time trial, losing to American Tyler Hamilton. Hamilton was later stripped of his medal for doping and Ekimov was promoted to gold. Ekimov joined the USPS team in 1997 as its first key international signing, briefly retiring in 2001 before rejoining the team the following year. In the 2003 Tour de France Ekimov placed 10th in the prologue. He was a key force in the winning team time trial effort in stage four and was important to Lance Armstrong's fifth Tour victory both on the flats and in the mountains. He missed the 2005 Tour de France due to injuries received in a training ride with Armstrong in Texas. During the final stage of the 2006 Tour de France, now racing for the Discovery Channel Pro Cycling Team, he announced that the 2006 Tour would be his last. He was honored by the peloton on the final stage, who allowed him to lead them over the line on the first of the eight laps of the Champs-Élysées. Ekimov started and finished 15 Tours de France, tying him with Lucien Van Impe for the second most Tour finishes, behind Joop Zoetemelk and Sylvain Chavanel. In September 2006 he finished riding for Discovery, but stayed with the team as Assistant Directeur Sportif to Johan Bruyneel. He helped guide the Discovery riders during the U.S. Pro Cycling Championships in 2006 as well as the Tour of California and the Tour de Georgia. On 9 September 2009, it was announced he would join as Directeur Sportif. In October 2012, he was announced as the general manager of the Russian. The UCI, in a letter written to Katusha Team, denied them entrance into the 2013 World Tour. Among the many ethical violations the UCI cited, the appointment of Ekimov was among them for reasons unspecified. After the end of 2016 season Ekimov stepped down from the role.
