Many believed Rossi would not win another championship on a less competitive Yamaha bike, but Rossi proved them wrong. Having taken chief engineer Jeremy Burgess with him, Valentino was to look forward to many positive things.
With the traditional first race of the season at Suzuka off the list due to safety considerations following the fatal accident of Daijiro Kato, the 2004 season started at Welkom in South Africa. Rossi won the race, becoming the only rider to win consecutive races with different manufacturers, having won the final race of the previous season on the Honda. Rossi would go on to win eight more GPs in the season, primarily battling Sete Gibernau, with Rossi clinching the championship at the penultimate race of the season at Phillip Island. Rossi ended the season with 304 points to Gibernau's 257, with Max Biaggi 3rd with 217 points.
In 2005 Grand Prix motorcycle racing season, Rossi captured his 7th World Championship and 5th straight MotoGP Championship. He finished with a total of 367 points, 147 points ahead of 2nd place finisher Marco Melandri (220 points), and Nicky Hayden finishing 3rd with 206 points.
The 2006 MotoGP season started off with Rossi, once again, being the favorite to take the Championship, but he had trouble in the first half of the season. Hayden held the points lead throughout most of the season, but Rossi was slowly working his way up the points ladder. It was not until Motegi when Rossi finally grabbed 2nd in the points race behind Hayden. In the Portuguese Grand Prix, the penultimate race of the season, Hayden was taken out by his teammate, Dani Pedrosa, and did not finish the race. This led to Rossi taking the points lead with only one race left in the season. However, Rossi crashed early in Valencia, the last race, and Hayden went on to win the 2006 MotoGP Championship. Rossi finished the season in 2nd place.
Rossi returned to MotoGP for the 2007 season riding the new Yamaha YZR-M1 800 cc. In the first race in Qatar he came second to Casey Stoner on the Ducati Desmosedici. In the second round of the season Rossi won the second race of the season in Spain, and would win 3 more races that season. Stoner dominated the season, winning 10 races to take his first title, 125 points clear of second place Dani Pedrosa. Pedrosa’s win in the last race at Valencia combined with Rossi’s retirement meant that he beat Rossi into third place by a single point. This was Rossi’s lowest championship position since his first season in 1996 in 125s. His bike lacked competitiveness, particularly in top speed compared to the Honda or Ducati, and he threatened to leave Yamaha if they are unable to deliver a better package.
For 2008 Rossi changed to Bridgestone tyres. The season started slowly with a fifth place finish in Qatar, but he took his first win in Shanghai, and also won the next two races. From that race, Rossi was on the podium of every remaining race (except the Dutch round at Assen, where he crashed on the first lap and finished 11th), winning a total of nine races in the season. His victories at Laguna Seca (after a pass down the “Corkscrew” corner over Stoner, who crashed but continued and took the second place) and at a rain-shortened race in Indianapolis, meant that Rossi has won in every current circuit in the calendar. His win in Motegi was his first victory there on a MotoGP bike. The victory at Motegi won Rossi his first 800cc MotoGP title, his sixth in premier category, and eighth overall.
On June 8, 2009, Valentino Rossi rode a Yamaha around the famous Isle of Man TT Course in an exhibition lap along-side fellow Italian motorcycle legend Giacomo Agostini, in what was called 'The Lap of the Gods'.
The 2009 season saw Rossi win 6 races to win his 9th championship title, beating his team-mate Jorge Lorenzo into second place by 45 points. 6 wins was the lowest number of wins Rossi has had in a championship winning season; the previous lowest was 9 in 1999 in the 250 cc class and 2003, 2004 and 2008 in MotoGP.
His victory at the 2009 Dutch TT in Assen was Rossi's 100th victory, becoming only the second rider in motorcycle grand prix history to reach 100 wins.
The 2010 season began with Rossi topping most of all pre-season testing sessions and took victory in the first race of the season in Qatar, after early leader Casey Stoner crashed out. Rossi injured his shoulder and back while training on a motocross bike after the Japanese Grand Prix was postponed to October due to the disruption to air travel after the second eruption of the Eyjafjallajökull volcano in Iceland. The following two rounds Rossi was beaten by team-mate Lorenzo with Rossi complaining about shoulder pain. The injury was not taken seriously initially and was expected to cure in a few weeks, but did not turn out as expected and the ligament tear in the shoulder failed to sufficiently heal.
On 5 June 2010 at his home race at Mugello, Rossi crashed in the second free practice session, around the Biondetti corner, at around 120 mph (190 km/h). Rossi suffered a displaced compound fracture of his right tibia, and after post-surgical care close to his home in the hospital at Cattolica, it was diagnosed that he was likely to be out for most of the season. It was the first time that Rossi had missed a race in his Grand Prix career. However ahead of the British Grand Prix, Suzi Perry reported in her Daily Telegraph column that Rossi was planning on making a comeback at Brno. This was confirmed a week later by Rossi himself. On 7 July, Rossi rode at Misano on a Superbike World Championship-specification Yamaha YZF-R1 provided by the Yamaha World Superbike Team to test his leg's recovery. He completed 26 laps during two runs, with a best lap time that was around two seconds off the pace of recent World Superbike times at the circuit. At the conclusion of the session, Rossi complained of discomfort, reporting pain in both his leg and his shoulder. On 12 July, Rossi took part in another test at Brno, after which Rossi stated he was happier and a lot more in form. After an observation by the Chief Medical Officer on the Thursday before the weekend, Rossi made his return at the German Grand Prix, two rounds earlier than predicted and only 41 days after the accident. He managed to end the race in fourth place after a battle with Casey Stoner for third. He added another race victory to his name at Sepang, Malaysia on his way to collecting 10 podiums throughout the whole season, including five podiums in a row in the final run in of the season, where he finished third in the overall standings.