In 1990, following a change in NHRA rules, Bernstein began to drive in the Top Fuel Dragster class. Two years later, Bernstein became the first driver in any class to exceed 300 MPH in competition, and won his first Top Fuel championship in 1996, becoming the first driver in NHRA history to win a championship in both of the nitro classes, however, Bernstein states that his 1996 championship was "somewhat tainted" due to the loss of driver Blaine Johnson. At the awards banquet that year, Bernstein gave up his championship trophy to Blaine's brother, and lifelong crew chief, Alan, who has gone on to win twelve more championship trophies himself, as crew chief for Gary Scelzi, Tony Schumacher, Larry Dixon, Del Worsham, Shawn Langdon and Brittany Force. Bernstein reclaimed the title in 2001, and is the only driver to have achieved multiple championships in both nitro categories.