[8] Duggan's collegiate debut came in the Frogs' 2019 season opener, a 39–7 home victory over the Arkansas-Pine Bluff Golden Lions when he came on in relief of starter Alex Delton late in the first quarter, scoring his first career rushing touchdown on his first possession.
[12][13] Prior to Duggan's sophomore season in 2020, a medical screening that was part of enhanced safety protocols associated with the COVID-19 pandemic revealed that he had been born with Wolff–Parkinson–White syndrome, a condition that affects the electrical system of the heart.
[15] Despite these medical ordeals, he was ready to play in the Frogs' 2020 season opener, throwing for 241 yards and three touchdowns against the Iowa State Cyclones.
[18] TCU finished with a 6–4 record and accepted an invitation to play the Arkansas Razorbacks in the Texas Bowl, but the game was canceled as part of the second wave of the pandemic.
He did throw for a career-best 346 yards and four touchdowns against the 4th-ranked Oklahoma Sooners,[21] but he was hampered by injuries for much of the season as he played through a broken bone and torn tendons in one of his feet.
[14] In a late October road loss against the Kansas State Wildcats that dropped the Frogs' record to 3–5, Duggan was benched when his injuries severely limited his productivity.
[24] In August, the quarterback competition that lasted throughout the spring and summer ended when Dykes and offensive coordinator Garrett Riley informed Duggan that Morris would be the starter.
Rather than entering the transfer portal to find a new program, Duggan elected to remain at TCU and told Dykes that he intended to be the best backup quarterback in the country and that he'd do anything to help Morris succeed.
[25] After throwing for a career-high 390 yards in a win over the Tarleton State Texans and going on the road to reclaim the Iron Skillet from crosstown rivals, the SMU Mustangs, to finish the non-conference schedule 3–0, Duggan and the Frogs made a statement with a resounding 55–24 victory over the 18th-ranked Oklahoma Sooners.
Down by 11 in the 4th quarter, Duggan led TCU on yet another comeback, scoring on an 8-yard touchdown run with 1:51 remaining to put him over 100 rushing yards for the game and connected with tight end Jared Wiley on the 2-point conversion to force overtime.
The Wildcats prevailed in OT[34] – but the next day, 12–1 TCU became the first team from the state of Texas to be selected to play in the College Football Playoff.
First, on July 12, 2023, he and Iowa State women's basketball star Ashley Joens were announced as the inaugural recipients of the Bob Bowlsby Award, honoring on- and off-field leadership and excellence and described by the Big 12 as "the Conference's most prestigious individual accolade".
[58] Battlehawks coach Anthony Becht had sought a quarterback with NFL practice squad experience after deciding not to retain the rights to incumbent A. J.