While he attended Spring Hill High School, Marlin played high school basketball and football, earning the captain status his senior year while he played quarterback and linebacker. He began his collection of civil war artifacts shortly after highschool. In 1976, he made his NASCAR debut at Nashville Speedway, filling in for his injured father in the #14 H.B. Cunningham Chevrolet. He started 30th and finished 29th after suffering oil pump failure early in the race. He made two more starts in 1978, finishing ninth at World 600 and twenty-fifth at Nashville for Cunningham. He ran Nashville again in 1979, finishing seventeenth. In 1980, he posted two top-tens, eighth in the Daytona 500 for Cunningham, and seventh at Nashville for D.K. Ulrich. From 1980 to 1982,Marlin was a three time track champion at the historic Nashville Speedway USA.
Marlin moved over to the #1 Bull's Eye Barbecue Sauce car owned by Hoss Ellington in 1986. His best finish that season came at the Firecracker 400, where he finished second. He got a full-time job in 1987, when he was hired by Billy Hagan to drive the #44 Piedmont AirlinesOldsmobile. He had four top-fives and finished eleventh in points. The following season, he had seven finishes of eighth or better in the first ten races and finished tenth in the standings. In 1989, the team received sponsorship from Sunoco and switched to the number 94. He tied a career-best thirteen top-ten finishes but dropped to twelfth in the final standings. He left the team at the end of the 1990 season. During the 1990 season, he won his first career Busch Series race at Charlotte, driving the #48 Diamond Ridge Chevrolet owned by Fred Turner.
Marlin signed to drive the #22 Maxwell HouseFord Thunderbird for Junior Johnson in 1991. He had a second-place finish at Daytona to start the season and won two poles at Talladega Superspeedway and the Firecracker 400, finishing seventh in the standings. The next season, he won an additional five poles and had six top-five finishes. Despite his career-high pole total, Marlin departed to drive the #8 Raybestos Ford for Stavola Brothers Racing. He had just one top-five finish and fell to fourteenth in the standings.
Marlin's first career win came in his 279th career start at the 1994 Daytona 500 driving for Morgan-McClure Motorsports in the #4 Kodak car. He went on to win the 500 again in the following year, becoming only one of three drivers to win consecutive Daytona 500s. The other two men that have accomplished that feat were Richard Petty and Cale Yarborough. He also became the only driver to have his first two career wins at the Daytona 500. Marlin won two more times during the 1995 season and finished a career high third in the point standings, during a four-year run with Morgan-McClure Motorsports. In 1997, he did not return to victory lane but dropped to twenty-fifth in the final standings. He left the #4 team at year's end.
In 1998, he joined SABCO Racing to drive the #40 Coors Light Chevrolet. He opened the season by winning the Gatorade 125, a qualifying race for the Daytona 500, but three weeks later, he failed to qualify for the Primestar 500, the first race he had missed since 1986. He finished in the top-ten six times and had a thirteenth-place points finish. In 1999, he won his first pole since 1995 at Pocono Raceway, but dropped down to sixteenth in the standings. In 2000, he won his second career Busch Series race, driving SABCO's #82 entry at Bristol Motor Speedway. During the season, he lost teammate Kenny Irwin, Jr. in a practice crash at New Hampshire International Speedway. After finishing in the top-ten seven times, he fell back to nineteenth in the overall standings.
In 2001, SABCO's majority ownership stake was purchased by CART (now IRL) championship owner Chip Ganassi and the team switched to Dodge Intrepids. In his first race with the new team, Marlin won the Gatorade 125 qualifying race at Daytona. Three days later at the Daytona 500, Marlin appeared to make contact with Dale Earnhardt, causing Earnhardt to crash head-on into the Turn 4 wall, an impact that would kill him. In the following days, Marlin and his family received hate mail and death threats from angry fans who felt that Marlin had killed Earnhardt. He was eventually publicly defended by two of Earnhardt's drivers, Dale Earnhardt, Jr. and Michael Waltrip, and was also cleared of any wrongdoing by NASCAR's investigation into the accident. He won Dodge's first race in its return to NASCAR at Michigan International Speedway, as well as winning the UAW-GM Quality 500. He tied his career best points finish of third that season.
Marlin scored two victories early in the 2002 season at Las Vegas Motor Speedway and Darlington Raceway. He led the 2002 Daytona 500 with six laps remaining until a red flag caution caused all drivers to have to stop and hold their positions. While waiting for the race to resume, Marlin climbed out of his car to look at the right front fender on his car. The fender was rubbing on the tire, and he pulled on it. Under NASCAR rules, no work of any kind is allowed to be performed on any car during a red flag caution period. Marlin was ordered to the back of the lead lap as a penalty. Ward Burton would go on to win, and Marlin finished eighth.
Marlin led the 2002 points standings for 25 straight weeks, holding a triple-digit advantage through most of the run. He lost the points lead to Mark Martin after the Sylvania 300, and would stand fourth in points going into the Protection One 400 at Kansas Speedway. During the race Marlin crashed and suffered a severe neck injury, causing him to miss the remainder of the season. His replacement, rookie Jamie McMurray, won the fall Charlotte race in his second start. Marlin called the victorious McMurray on national television minutes after the stunning win, congratulating McMurray and the team on prime-time television. He finished 18th in the final standings despite missing the final seven races. Marlin did not finish in the top-five in 2003, but had 11 top-tens and matched his previous year's finish of eighteenth in points. Despite three top-fives in 2004, he fell to 21st in points. During the 2005 season, Ganassi announced Marlin would be replaced by David Stremme for the 2006 season in order to attract the younger male demographic.
Marlin joined MB2 Motorsports for 2006 to drive the Waste Management Chevy, running with the #14 in tribute to his father, Coo Coo Marlin, who died during the 2005 season. Marlin's only Top 10 finish in 2006 was ninth place finish at Richmond. His 2006 season was shadowed by bad luck and #14 finished 36th in owner points.
Marlin was able to qualify via speed for each of the first five races of the 2007 season, his Pep Boys #14 team was the only team out of the top 35 from 2006 to do this. Marlin's run in the #14 ended on July 17, 2007, when Ginn Racing announced Regan Smith, who had been splitting time with Mark Martin in Ginn's U.S. Army-sponsored #01 car, would replace him beginning at the Allstate 400 at the Brickyard at Indianapolis. He attempted to qualify for two races in 2007, but he failed to qualify for either. He tried to make the Sharpie 500 at Bristol in the #78 car as a replacement for Kenny Wallace, and the UAW-Ford 500 at Talladega, replacing Mike Wallace in the #09 car. However in November he managed to qualify the #09 and drove at Phoenix for a 25th place finish, and a week later at Homestead finishing 33rd.
Marlin failed to qualify for the 2008 Daytona 500 in the #09 car, but qualified at Talladega and the following week at Richmond as well. For Darlington, Marlin raced in his old #40 car and qualified 14th, and also at the Coca-Cola 600 at Lowe's Motor Speedway in the #40, still in for the injured Dario Franchitti. He finished out the rest of the season driving for Phoenix Racing. In March 2009, Marlin participated in and won the Saturday Night Special, a charity event at Bristol Motor Speedway which included NASCAR Legends. He led the entire event in a car painted similar to the one he drove with Morgan McClure Motorsports, and wearing an older-style Coors Light uniform from his days while driving for Chip Ganassi. He will continue to drive part-time in the Sprint Cup Series for Phoenix.
For the 2009 NASCAR Sprint Cup Series, Marlin continued to run a limmited scheduel in the #09 Phoenix racing Miccosukee Resort & Gaming Chevrolet. His best finish for the '09 season thus far has been 35th at Martinsville.
An announcement was made preceding the Cup Series finale weekend at Homestead-Miami Speedway that Marlin would attempt the race in the #70 Chevrolet for TRG Motorsports. He announced that it would be his final race and that he would be retiring shortly afterwards.These plans were later denied by Marlin. They are not true and he has no plans to drive at Homestead at all.
Marlin currently has not announced his plans for 2010.