Baldwin began his crew chief career in 1997 with the No. 20 Hardee's Ford for Ranier-Walsh Racing. After Hardee's was acquired by CKE Restaurants and the sponsorship was pulled mid-year, the team shut down. Baldwin then became crew chief for car owner Junie Donlavey and driver Dick Trickle, helping the team achieve its first top-five finishes in three seasons. In the fall of 1998 he moved to Bill Davis Racing as crew chief for Ward Burton. The pairing won four races together, including the 2002 Daytona 500, before Baldwin's departure later that season.
In 2003 Baldwin became crew chief of the No. 7 Dodge Intrepid for Ultra Motorsports with Jimmy Spencer. He subsequently joined Evernham Motorsports as crew chief for Kasey Kahne, who won NASCAR Rookie of the Year honors in 2004 and earned his first race victory with Baldwin at Richmond International Raceway the following season. Between 2003 and 2004 Baldwin also fielded a Busch Series team that ran drivers including Wally Dallenbach Jr., Damon Lusk, Tracy Hines, and Paul Wolfe before being sold to Evernham after 2004. Baldwin later moved to Robert Yates Racing to work with Elliott Sadler.
On January 6, 2009 Baldwin announced the formation of Tommy Baldwin Racing, a Sprint Cup Series team running Toyotas. Scott Riggs drove the No. 36 for most of the early season before departing after the Coca-Cola 600. For much of 2009 TBR operated as a start-and-park team. The car earned a three-race sponsorship from Red Bank Outfitters and a single-race deal with Mahindra Tractors after qualifying for the Daytona 500.
In 2010 the team switched to Chevrolet and hired Mike Bliss as its primary driver. The team used a rotating roster of drivers across subsequent seasons, including Geoff Bodine, Steve Park, Johnny Sauter, Ron Fellows, Casey Mears, J. J. Yeley, and Dave Blaney. For 2011 Baldwin retained Blaney for a full season, and the team broke into the top 35 in owner's points for the first time in its three-year history after a 13th-place finish at Richmond. Blaney led late at both Daytona and Talladega in 2011 before being caught up in late-race incidents at each. In January 2012 Baldwin sold the owner's points from the No. 36 to Stewart–Haas Racing to secure a spot in the 500 for the No. 10 driven by Danica Patrick.
TBR's best finish was third place, achieved twice: Blaney's result at the October 2011 Talladega race, and a third-place finish at a rain-shortened Pocono race in August 2016 for Timmy Hill in the No. 7. The Cup team shut down after 2016, though it was briefly revived for the 2017 Daytona 500 with Elliott Sadler.
In 2017 Baldwin joined the newly formed Halmar Friesen Racing Truck team as team manager before departing later that year. He subsequently served as Competition Director at Premium Motorsports and as crew chief of the team's No. 15 Cup car. In 2019 he re-entered the NASCAR Cup Series with a part-time entry, beginning at Daytona. He later became Competition Director at Rick Ware Racing.
Baldwin's sons Jack and Luke compete in modified racing. In August 2023 Baldwin revealed he had been diagnosed with a treatable form of cancer, prompting a hiatus for his modified team.