The team was established in 1999 following the retirement of Wayne Rainey, who had previously managed a factory-supported Yamaha effort in the 500cc class. Before Rainey's involvement, legends including Kenny Roberts and Giacomo Agostini had each run their own works-supported Yamaha programs. The new factory structure gave Yamaha a consolidated, professionally managed entry suited to the evolving Grand Prix landscape.
Max Biaggi and Carlos Checa raced for the team from 1999 to 2002, with Biaggi accumulating eight race victories — first on the Yamaha YZR500 and later on the YZR-M1. In 2003, Checa was partnered with Marco Melandri in a season that yielded no podium finishes.
The transformation of the team's fortunes began in 2004 when Valentino Rossi joined Carlos Checa. Rossi immediately delivered nine wins and the riders' championship. With Colin Edwards arriving as his new teammate in 2005, Rossi won the championship again with eleven victories. The pair remained together through 2006, when Rossi earned five wins and finished runner-up in the standings.
In 2008, Yamaha formed one of the most high-profile pairings in MotoGP history when Rossi was joined by the young Jorge Lorenzo. Despite running from separate pit boxes — Rossi on Bridgestone tyres, Lorenzo on Michelin — the operation functioned as a unified team. Rossi dominated that season, winning nine of eighteen races and finishing on the podium in every race but two. Lorenzo, in his learning year, took victory at Estoril and finished fourth in the championship.
In 2009, Yamaha reached a new peak. Rossi claimed the riders' title and Lorenzo finished second; together they won twelve of the seventeen rounds, and Yamaha secured the Constructors' Championship. After seven years with the team, Rossi departed at the end of 2010 to join Ducati.
With Rossi at Ducati, Lorenzo carried the team forward. He won the riders' championship in 2015, the team's first title since Rossi's 2009 crown. Rossi had returned to Yamaha for the 2013 season, and in 2015 the pair again contested the championship together, with Lorenzo ultimately prevailing.
Following Lorenzo's departure to Ducati after 2016, Yamaha entered a difficult period of transition. The next world championship title did not arrive until 2021, when Fabio Quartararo — riding under the Monster Energy Yamaha MotoGP banner — claimed the riders' crown after a consistent and dominant campaign, ending the team's six-year wait.
Over its history, the Yamaha factory team has fielded some of the most celebrated names in Grand Prix motorcycle racing. Valentino Rossi alone won four of his nine world titles with the squad. The combination of Yamaha's YZR-M1 platform and the factory team's engineering and logistical support made it a perennial championship contender in the four-stroke MotoGP era from 2002 onwards.
Yamaha undertook significant technical development in the mid-2020s, testing a new V4 engine configuration at the Brno Circuit with test rider Andrea Dovizioso in July 2025. The V4 engine is expected to make its full competitive debut in 2026 across all four factory and satellite Yamaha entries, marking the most significant engineering shift for the marque since the transition from two-stroke to four-stroke machinery at the dawn of MotoGP.