2009

At the 2009 Japanese Grand Prix, Kobayashi competed in the first two free practice sessions in place of Timo Glock, who was ill.^[3] Glock recovered in time to take part in the third free practice session and qualifying, but was injured after crashing in the final session and had to miss the race. Toyota asked the Fédération Internationale de l'Automobile (FIA) for permission to run Kobayashi in the race, but this was refused as the regulations state a driver must run in at least one session on Saturday to be eligible to start the race.^[4]

Kobayashi made his Formula One debut at the 2009 Brazilian Grand Prix, following a complication to Glock's injury that was initially not detected.^[5] He qualified 11th in a chaotic session that lasted for over two and half hours and was red-flagged twice due to accidents caused by torrential rain. Early in the race, while running in sixth place, he held off for several laps a challenge by Jenson Button, who needed to finish well to clinch the world championship. He finished the race in tenth place, and was later promoted to ninth when Heikki Kovalainen was penalised. Button jokingly described Kobayashi as "absolutely crazy, very aggressive".^[6] He also competed in the 2009 Abu Dhabi Grand Prix, as Glock's injury had not healed sufficiently.^[7] Kobayashi qualified 12th and finished sixth, scoring his first World Championship points, in the inaugural day-night race in Abu Dhabi.^[8] Before Toyota decided to withdraw from Formula One, Kobayashi was expected to be given a full-time seat at Toyota for the 2010 Formula One Season.^[9]

2010

Following Toyota's withdrawal, Kobayashi faced an uncertain future, but he was mentioned in lists of probable drivers for the series' new teams for 2010.^[10] After weeks of speculation, it was confirmed on December 17, 2009, he would drive for Sauber for the 2010 season. Despite the team having been sold by BMW back to founder Peter Sauber after the 2009 season, and no longer using BMW components, the team was still named BMW Sauber as it had been known for the past four seasons.^[11] His teammate was former McLaren tester Pedro de la Rosa. Kobayashi completed his first laps in the new Sauber C29 chassis during F1 winter testing on 2 February.

During the Australian Grand Prix, a front wing failure on his Sauber caused him to hit the barrier, rebounding off it to cause a three-car crash taking out Nico Hülkenberg and Sébastien Buemi. In the next race in Malaysia he qualified in ninth place, his best grid position up to that point, however he suffered an engine failure early in the race. In China, Kobayashi was involved in a three-way collision with Buemi and Vitantonio Liuzzi on the first lap, making him the only driver to retire from the first four races. In Turkey, he won his first points of the season, coming home tenth after being promoted a place due to Vettel's retirement after a collision with teammate Webber and Petrov's puncture. In Valencia, he finished seventh by passing both Fernando Alonso and Sébastien Buemi in the final laps on fresh tyres, after driving the majority of the race in third position on his first set of tyres. He followed that with sixth place in Silverstone, eleventh in Germany, ninth in Hungary and eighth in Belgium.

At the Italian Grand Prix, Kobayashi suffered a gearbox failure and retired from the Singapore Grand Prix after hitting a track-side barrier. Kobayashi's teammate changed in Singapore as Pedro de la Rosa was removed in favour of Nick Heidfeld. In Japan, Kobayashi qualified 14th and finished seventh, passing several drivers along the way including his teammate, in a very impressive fashion. He finished eighth in Korea and tenth in Brazil, eventually finishing the season with 32 points. In his review of the season, former TV commentator Murray Walker stated that Kobayashi is "without a doubt Japan's best [F1 driver] yet".^[12] Kobayashi gained a reputation during the season as a highly skilled overtaker, being able to outbrake drivers several car lengths in front of him. His aggressive overtaking style was described by Martin Brundle as, "He gets to the normal braking point and then goes, 'Now, which one is the brake again? That's right, it's on the left,' and he just sails past people!"^[13] He qualified well against his more experienced teammates, outqualifying de la Rosa and Heidfeld 11 times to 8 over the season.

2011

Kobayashi remained with Sauber (renamed from BMW Sauber to Sauber F1 Team) in 2011,^[14] where he was partnered by GP2 graduate Sergio Pérez. Kobayashi finished eighth in the season opening Australian Grand Prix, but he and Pérez – who had finished seventh – were disqualified after the race due to an irregularity with the car's rear-wing. The next race of the season in Malaysia was another strong showing for Kobayashi, finishing eighth in the race, eventually classified seventh after Lewis Hamilton received a penalty. He finished tenth in his next three races, before a career-high fifth place in an incident-packed Monaco Grand Prix. In an extremely wet Canadian Grand Prix, Kobayashi worked his way up from 13th place to 2nd having not decided to change to extreme wet tyres before the race was red-flagged, as many other drivers had. This essentially gave him a free pit stop while the race was suspended. After the restart, the track began to dry out, and after changing to intermediate tyres and finally slicks, Kobayashi dropped several places, including having a spin whilst lapping a backmarker and being rear-ended by Nick Heidfeld. He eventually finished seventh, 0.045 seconds behind Felipe Massa, who passed him on the final straight.

2012

On 28 July 2011, it was announced that Kobayashi would remain with Sauber into the 2012 season, alongside teammate Pérez.^[15]

Kobayashi started the season with sixth place at the Australian Grand Prix,^[16] and a retirement at the Malaysian Grand Prix, due to a problem with his car's brakes.^[17]

He then started third at the Chinese Grand Prix behind the Mercedes of Nico Rosberg and Michael Schumacher. He dropped to tenth but managed to set the fastest lap. At the Spanish Grand Prix he finished fifth after overtaking Jenson Button and Nico Rosberg. Kobayashi finished in the points once in the next four races, finishing ninth in Canada. Kobayashi finished in a then-career-best fourth place at the German Grand Prix – having finished fifth on-the-road – as he was helped by a post-race penalty for second-placed Sebastian Vettel.^[18] After retiring late in the race at the Hungarian Grand Prix, Kobayashi qualified a career-best second for the Belgian Grand Prix but was caught in a first-corner accident along with four other drivers. Kobayashi was the only one of the five to continue in the race, and finished thirteenth.^[19]

Kobayashi took his maiden podium in Formula One with third place at the Japanese Grand Prix, after lasting through race-long pressure from Jenson Button. Kobayashi became the first Japanese driver to finish on a Formula One podium in Japan in 22 years, after Aguri Suzuki in the 1990 Japanese Grand Prix, and was the third Japanese driver to finish on a Formula One podium after Suzuki and Takuma Sato in the 2004 United States Grand Prix.^[20]

On 23 November 2012, Sauber announced that Kobayashi would not be a part of the team's line-up for the 2013 season, as Nico Hülkenberg and Esteban Gutiérrez would form the race team and Robin Frijns as reserve driver.^[21] Kobayashi ultimately finished the season in twelfth place in the Drivers' Championship, with 60 points.^[22] Despite raising around €8 million in sponsorship, Kobayashi elected to focus on gaining a competitive drive for the 2014 season rather than a 2013 drive.^[23]