Ekström debuted in karting in 1993. He then competed in the Renault 5 Turbo Cup, winning the championship in 1996. He entered the Swedish Touring Car Championship in 1997, finishing runner-up with a Volvo 850. In 1998, driving a Ford Mondeo, he claimed four podiums. He won the 1999 championship driving an Audi A4 quattro. He switched rides again in 2000, finishing third with a factory Volvo S40.
In 2001, Ekström joined the Abt Junior team to compete at the Deutsche Tourenwagen Masters. Driving an Audi TT, he finished eighth in his debut season, third in 2002, and fourth in 2003. In 2004, Ekström won the DTM championship, defeating Mercedes rivals Gary Paffett and Christijan Albers. He finished second behind Paffett in 2005. After a difficult 2006 season, Ekström won his second DTM title in 2007. He announced his retirement from DTM in January 2018 to concentrate on running his rallycross team with added support from Audi Sport.
At the 2005 Race of Champions, Ekström won the Nations' Cup with Tom Kristensen. In 2006, he won the Henri Toivonen Memorial Trophy and earned the title Champion of Champions by defeating Sébastien Loeb in the individual event finals. He won the 2007 Race of Champions, beating Michael Schumacher in the individual finals. In 2009, he won the Race of Champions once more, again beating Schumacher in the final.
Ekström debuted in the World Rally Championship in 1999. His best WRC result came at the 2005 Swedish Rally, where he finished tenth in a Škoda factory team Fabia WRC.
Ekström became the first Scandinavian driver to take part in the NASCAR Sprint Cup Series in June 2010. He raced for Team Red Bull at Infineon Raceway, substituting for Brian Vickers in the No. 83 Toyota Camry while Vickers was inactive due to blood clots. Ekström finished 21st, leading seven laps and remaining in the top-five or top-ten for much of the race. His result was equalled by fellow Scandinavian Jan Magnussen from Denmark, who also competed in the same race and finished ahead of Ekström. Ekström also ran the Air Guard 400 at Richmond International Raceway, starting 42nd and finishing 31st.
Ekström competed in the Bathurst 1000 in 2013 alongside Andy Priaulx in a wildcard entry. The entry qualified nineteenth and finished tenth. Commentator Mark Skaife, a former 1000 winner, hailed his efforts, stating he was "one of the best debutants I have seen" and "the best international driver since Jacky Ickx". Ickx won the race on debut with Allan Moffat in 1977.
Ekström followed in the footsteps of his father Bengt by branching into rallycross in 2013, competing in the Swedish round of the European Rallycross Championship at Höljes and finishing second in a Volkswagen Polo. He subsequently established his own EKS RX team to compete in the FIA World Rallycross Championship. The team debuted at the Norwegian round of the 2014 World Rallycross Championship season in Hell, fielding a pair of Audi S1s for Ekström and 2013 Junior World Rally Champion Pontus Tidemand.
Following Audi's withdrawal of its works programme at the end of 2018, some of the team's Audi S1s were sold to privateers. The team continued as a one-car privateer operation after signing Krisztián Szabó from Hungary, with Ekström making a wildcard entry at the inaugural World Rallycross event at Spa-Francorchamps.
Ekström returned to the World Rallycross Championship in the 2020 season, initially as a wildcard for the first two rounds in Sweden for the JC Race Teknik team — which was running two former EKS RX Audi S1s. He replaced Latvian Jānis Baumanis, who was unable to complete the full season due to funding issues caused by the COVID-19 pandemic. Ekström signed with the team for further double-header rounds in Finland and Latvia, achieving two wins and five podiums from six events and becoming a championship contender alongside fellow Swede Johan Kristoffersson.
Ekström joined Cupra x Zengő Motorsport for the inaugural season of Pure ETCR (later rebranded as FIA ETCR). He won Cupra's home event in Spain and finished on the podium at all other races, earning the drivers' title and securing the teams' title for Cupra. He also competed in the Extreme E electric off-road championship with the Abt Cupra team. He later joined the Acciona Sainz Extreme E team as male driver, replacing Carlos Sainz, who was recovering from a Dakar accident. The team finished third in the 2023 Extreme E season. Ekström subsequently joined the McLaren Extreme E team, but that cooperation did not last as the championship was cancelled mid-season.
In 2021, Ekström made his first Dakar Rally attempt with a Yamaha side-by-side car. The race was riddled with technical issues. In 2022, with navigator Emil Bergkvist, he competed in the Audi RS Q e-tron rally-raid car, won one stage, and finished ninth overall. He also competed for Audi in the 2023 Dakar, where all three Audi cars suffered misfortunes; Ekström finished fourteenth. The 2024 Dakar Rally was Ekström's final race with Audi; a technical issue ended his contention, and for the remaining stages he acted as a support car for teammate Carlos Sainz, who claimed overall victory.
On 1 October 2024, Ekström announced his move to the M-Sport Ford team for their Dakar programme. The 2025 Dakar Rally, contested in the newly built Ford Raptor T1+, saw Ekström and Bergkvist climb into the top three early, win one stage, and finish third overall. The crew repeated third place overall at the 2026 Dakar Rally.
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