In 1996, Burton left the Stavola Brothers for Roush Racing. Driving the #99 Exide Batteries-sponsored Ford for his new team, he finished 13th overall in the season points standings despite failing to qualify for the Purolator 500 in March as a new team (provisionals in the first four races were based on 1995 points, and Burton's team did not have points from 1995). His career hit a peak from 1997 to 2000, as he never finished lower than fifth in the points standings.
He achieved his first career win in 1997 in the Interstate Batteries 500 at Texas Motor Speedway (the inaugural NASCAR race at the track), and would go on to win 14 more races during the four-year run.
In 1999, Burton won a career-high six races, including the Jiffy Lube 300 for a third straight year, and clinched two of the series' four majors (Coca-Cola 600 and the 50th Annual Southern 500), which would lead to a fifth-place finish in points. His best points finish was in third in 2000, just 294 points behind champion Bobby Labonte.
On September 17, 2000, Burton led every lap of the Dura Lube 300 at New Hampshire International Speedway, in unique circumstances (this race was the only Loudon race to use a restrictor plate, imposed for safety reasons after the deaths of Adam Petty and Kenny Irwin, Jr. earlier in the year at the track). From 1997 to 2000, Burton won an event at NHIS every year.