2000 marked Houston's first start in the Winston Cup Series as he competed in five races to prepare for his 2001 rookie campaign with PPI Motorsports. Out of the five races his best finish would come at Lowe's Motor Speedway, a 26th. Houston began the 2001 year well with a 9th place qualifying effort at the Daytona 500 in the #96 McDonald's Ford. It would be one of the highlights of the year, as Houston ended the year with no top 10s and a best finish of 17th at Martinsville; Houston only managed to qualify for 17 races and his team folded after McDonald's pulled its sponsorship late in the season. He has not returned to the Cup Series since.
In 1997, Houston made his first Craftsman Truck Series start with Addington Racing. He would compete in four races for the team with a best finish of 11th at Martinsville. For the 1998 season, he returned to Addington Racing and ran full-time in the Truck Series. Houston would have a solid year winning his first race at New Hampshire International Speedway and posting 9 top tens, while finishing 12th in points. Houston again returned to Addington Racing for the 1999 season and he scored 14 top tens with an 8th place finish in points. 2000 was a breakout year for Houston, as he won two races at Homestead and Portland, had 13 top fives, and 18 top tens, finishing 3rd in points to Roush Racing Teammates Greg Biffle and Kurt Busch. He returned to the series in 2002 with Melling Racing where he ran one race at South Boston Speedway. After that Billy Ballew Motorsports hired him to run the remainder of 2002. He would post a best finish of 12th at California out of the five races he competed in. In 2003, Houston was still running races for Billy Ballew and Nelly when Vokal became his primary sponsor, until Billy ran out of money to run two trucks. Ballew kept Rich Bickle, leaving Houston without a ride. Later that year, Ultra Motorsports gave him a truck ride and he did very well, finishing no worse than sixth and earned a pole at Texas Motor Speedway. For the 2004 season, he continued driving for Ultra Motorsports until he was released after the race at Bristol. Andy's best finish with the team that year was a 7th at Dover. For the remainder of 2004 with the exception of Richmond, Houston raced with multiple teams, but with limited success. In 2005, he only ran one race with Key Motorsports at Bristol Motor Speedway, finishing 33rd after a crash. He has yet to return to the NASCAR Camping World Truck Series as a driver since that race.