Bowyer began racing at the age of five in motocross racing. He went on to capture over 200 wins and numerous championships over the next eight years. In 1996, he began racing street stocks at Thunderhill Speedway in Mayetta, Kansas, and won the Modified championship there in 2000. Clint racked up 18 wins and 32 top-five finishes on his way to capturing the 2001 Modified championships at Lakeside Speedway in Kansas City, Kansas and Heartland Park Topeka.
In 2002, he began racing in the NASCAR Weekly Racing Series, posting 9 poles, 12 wins and 32 top-five finishes en route to a second place finish in the NASCAR Weekly Racing Series national point standings. He was also crowned the 2002 NASCAR Weekly Racing Series Midwest Champion after another Modified championship at Lakeside Speedway and a Late Model championship at the famed I-70 Speedway in Odessa, MO, his first attempt at racing on asphalt.
In 2003, Bowyer raced a full season in the NASCAR AutoZone Elite Division Midwest Series, scoring one top-ten finish in 11 starts. He also would make his first ARCA starts in 2003, and caught the eye of legendary car owner Richard Childress after leading 47 laps and finishing second in his debut at Nashville Superspeedway.
In 2004, Bowyer shared seat time in the #21 Reese's Chevrolet with Kevin Harvick, driving in half of the 34 Busch Series races that year. He had 1 pole and 7 top tens, and attained a season-high 3rd place finish in the Federated Auto Parts 300, a Nashville Superspeedway race in June. He also ran 3 races for Kevin Harvick, Inc. with help from Andy Petree Racing. Bowyer's first full season was in 2005, replacing Ron Hornaday in the #2 ACDelco Chevrolet. He won two poles and two races en route to a second place finish to repeat-champion Martin Truex Jr., losing only by 68 points
Bowyer made his NEXTEL cup debut in the Sylvania-sponsored #33 Chevy on April 23, 2005, during the Subway Fresh 500 at Phoenix International Raceway. He finished 22nd as the first car one lap down. During his successful season in the Busch Series, Richard Childress Racing announced on October 15, 2005, that Bowyer would race the #07 Chevrolet full time in the NEXTEL Cup series, replacing Dave Blaney in the 2006 season.
Bowyer began his rookie Cup season with three top-fifteen finishes and had a total of eleven top-tens that season, his best finish a 3rd at California Speedway. He finished 68 points behind Denny Hamlin for NASCAR Rookie of the Year honors. He also continued to drive the #2 in the Busch Series full-time, winning once and finishing 3rd in points. Bowyer won his first Craftsman Truck Series Truck Series race in the #46 Jack Daniel's Chevrolet fielded by Morgan-Dollar Motorsports at Texas Motor Speedway on November 3, 2006, in his third career start.
In 2007, Clint is running a partial Busch Series schedule in the RCR #2 car with BB&T sponsorship, as well as selected races in the NASCAR Craftsman Truck Series for Kevin Harvick.
On the last lap of the Nextel Cup 2007 Daytona 500, Bowyer's car flipped upside down during a multi-car crash in the final lap. The car skidded along the track, hood to the pavement, for several yards, eventually crossing the finish line in that condition. Shortly afterward, the car flipped back onto its tires, and Bowyer escaped the driver's seat with the engine on fire under the hood in front of him. In a funny moment, after exiting the wreck, Bowyer calmly threw his racing gloves back in the burning car and looked up at the scoring pylon to see what position he had wound up in, which turned out to be 18th.
On April 20, 2007, Bowyer won the Busch Series Bashas' Supermarkets 200 at Phoenix International Raceway. He followed that up with another Busch Series win on May 4 in the Circuit City 250 at Richmond International Raceway.
On May 11, 2007, Bowyer won the Budweiser Pole position for the Dodge Avenger 500 at Darlington Raceway. It was the first career pole award in the NEXTEL Cup Series for Bowyer.