The team was established in 1999 following the retirement of Wayne Rainey, who had run a factory-supported 500 cc squad in the preceding years. Max Biaggi and Carlos Checa were the first riders under the new structure, racing together from 1999 to 2002. Biaggi collected eight race victories during that period, initially aboard the Yamaha YZR500 two-stroke and then switching to the YZR-M1 four-stroke in 2002 when the MotoGP class was introduced. In 2003, Checa was joined by Marco Melandri but the team endured an average campaign without podium finishes.
Yamaha's fortunes changed dramatically when Valentino Rossi joined for 2004, having moved across from Honda. Rossi won nine races and claimed the championship in his debut season with the team. In 2005, with Colin Edwards as his partner, Rossi repeated the title with eleven victories. Rossi and Edwards remained together through 2006 and 2007; Rossi added five more wins in 2006 to finish second in the championship and four wins in 2007 to finish third.
For 2008, Yamaha fielded a distinctive pairing as rookie Jorge Lorenzo joined Rossi. The two operated from separate pit boxes — Rossi running Bridgestone tyres while Lorenzo continued with Michelin — but functioned under the same team structure. Rossi dominated the season, winning nine of eighteen races and finishing on the podium in all but two rounds. Lorenzo won at Estoril in his debut year and finished fourth overall. In 2009 Yamaha produced their strongest campaign to date: Rossi won the riders' title and Lorenzo finished second, the pair combining to win twelve of seventeen races while Yamaha secured the Constructors' Championship.
After seven years with the factory team, Rossi departed for Ducati at the end of 2010.
Jorge Lorenzo became Yamaha's lead rider and delivered the 2010 and 2012 championship titles. Rossi returned to Yamaha for 2013 after two difficult seasons at Ducati. Together they formed one of the most celebrated pairings on the grid through the mid-2010s. Lorenzo claimed a further world title in 2015 before departing to Ducati.
After six years without a Riders' title following Lorenzo's 2015 championship, Yamaha ended their drought in 2021 when Frenchman Fabio Quartararo won the championship, becoming Yamaha's first non-Spanish or non-Italian title holder in the modern era.
For the majority of the MotoGP era, Yamaha's YZR-M1 used an inline four-cylinder engine layout, a configuration that gave the machine a reputation for outstanding handling and corner-speed, even if outgunned on straight-line velocity by some rivals. In 2025, Yamaha began testing a new V4 engine configuration with Andrea Dovizioso as test rider at Brno Circuit. The V4 layout is scheduled to make its full competitive debut in 2026, with both the factory team and satellite Pramac Racing squad set to use the new specification.
Yamaha is among a handful of manufacturers to have won the MotoGP Riders', Constructors', and Teams' championships across multiple seasons. The factory team's association with Valentino Rossi — widely considered the greatest MotoGP rider of all time — defines much of its historical identity. The team's Italian base and multinational rider roster reflect the international structure that underpins Japanese manufacturers' European racing programs, a model established in the early 2000s as the premier class transitioned from two-stroke to four-stroke machinery.