Following the 1998 24 Hours of Le Mans, where both BMW V12 LMs failed to finish due to mechanical difficulties and aerodynamic inefficiencies, BMW Motorsport decided to revamp their sportscar project. They replaced the V12 LM with a new car, the V12 LMR, for 1999. The V12 LMR retained only the basic structures of the V12 LM; all of the car's bodywork was redone from scratch. The cooling ducts were moved to the top of the car, instead of from the bottom, where they had suffered from ambient track heat.
The V12 LMR featured a small roll hoop located only behind the driver's seat, taking advantage of a loophole in the ACO's Le Mans prototype regulations. This design reduced drag and obstruction for air to the rear wing. Williams Racing built four new chassis. The car retained the BMW S70/3 5990 cc V12 engine. Responsibility for running the cars was handed over to Schnitzer Motorsport.
The V12 LMR debuted at the 12 Hours of Sebring, where BMW Motorsport and Schnitzer Motorsport entered two cars. The cars took pole position in qualifying. During the race, both cars ran towards the front for the first six hours. Chassis #001 had a large accident, damaging the car beyond repair. The second V12 LMR took the overall win.
The team prepared for Le Mans with a test session in May, where three V12 LMRs appeared. One car featured a paint job created by artist Jenny Holzer. In the practice session, a V12 LMR took the fourth-fastest lap time, behind two Toyota GT-Ones and a Panoz prototype.
At the 24 Hours of Le Mans, the V12 LMRs ran strong, outlasting competitors like Mercedes-Benz, Nissan, Toyota, and Audi. In the closing hours, the #17 BMW V12 LMR driven by JJ Lehto crashed heavily due to a stuck throttle. The #15 V12 LMR took the lead and secured the victory, driven by Joachim Winkelhock, Pierluigi Martini, and Yannick Dalmas. The BMW V12 LMR reached 342 km/h (214 mph) on the Mulsanne Straight, producing approximately 580 hp.
After Le Mans, the team returned to North America for the American Le Mans Series season. They won at Sears Point and secured two more victories over the final four races. Despite four wins, BMW lost the team championship to Panoz by two points.
In 2000, BMW's alliance with Williams brought the marque into Formula One. BMW decided to concentrate on Formula One and not return to Le Mans. However, they decided to run the full American Le Mans Series season before retiring the cars.
At Sebring, the BMWs qualified in 5th and 6th positions, behind both Audis and Panoz LMPs. The BMWs finished 3rd and 4th. They achieved victories at Charlotte and Silverstone. At the Nürburgring, the V12 LMR lost to a Panoz.
The V12 LMR consistently finished second to the dominant Audi R8 throughout the next four rounds. For Petit Le Mans, BMW brought out chassis #004, the Art Car. The Art Car finished fifth.
BMW did not participate in the final round in Australia, retiring the cars and concluding their ALMS campaign. They finished second in the team's championship behind Audi.