In 2015, Naughton's freshman year at Virginia Tech, he pitched 44 innings, going 2–1 with a 4.91 ERA and 35 strikeouts. As a sophomore in 2016, he appeared in 15 games (making 14 starts) in which he compiled a 3–7 record and a 6.75 ERA.[4] That summer, he played in the Cape Cod Baseball League for the Harwich Mariners and was named a league all-star.[5][6][7] In 2017, as a junior at Virginia Tech, he pitched in 17 games (seven starts) in which he went 2–6 with a 6.24 ERA, striking out 63 batters in 57+2⁄3 innings.[8] After his junior year, he was selected by the Cincinnati Reds in the ninth round of the 2017 Major League Baseball draft.[9]
On August 4, 2021, the Angels selected Naughton's contract and promoted him to the major leagues.[26] At the time of his promotion, he had a 5.34 ERA over 55+2⁄3 innings pitched between Rocket City and Salt Lake.[27] On August 8, he made his major league debut in relief at Dodger Stadium against the Los Angeles Dodgers, giving up one run, one hit, and two walks over one inning.[28] On September 1, 2021, against the New York Yankees, Naughton made his first career start, pitching 3+2⁄3 innings, allowing three runs and striking out two.[29] Naughton finished the 2021 season with the Angels appearing in seven games (five starts) in which he went 0–4 with a 6.35 ERA, 14 walks, and 12 strikeouts over 22+2⁄3 innings.[30]
On March 18, 2022, Naughton was designated for assignment by the Angels.[31]
St. Louis Cardinals
On March 21, 2022, Naughton was claimed off waivers by the St. Louis Cardinals and joined the club's 40-man roster.[32] He was assigned to the Memphis Redbirds of the Triple-AInternational League to begin the 2022 season.[33] Naughton made his debut with the big league club on April 26, 2022, and pitched 1+1⁄3 scoreless innings against the New York Mets in a 0–3 loss.[34] Naughton made 26 appearances for the Cardinals, logging a 4.78 ERA with 31 strikeouts and 1 save in 32.0 innings pitched.
Naughton made the Cardinals' Opening Day roster in 2023, as part of the team's bullpen.[35] He made 4 scoreless appearances for St. Louis before leaving an outing against the Milwaukee Brewers on April 8 with an injury.[36] He was placed on the 60-day injured list on May 17 with a left forearm strain.[37] On June 28, Naughton underwent season–ending surgery to repair the flexor tendon in his left elbow.[38] On November 14, Naughton was removed from the 40–man roster and sent outright to Triple-A Memphis.[39]
Naughton made 15 rehab appearances for Memphis, the Single–A Palm Beach Cardinals, and the rookie–level Florida Complex League Cardinals in 2024. In July 2024, Naughton underwent ulnar collateral ligament reconstruction surgery, having also re–tore the flexor tendon he tore in 2023.[40] On March 28, 2025, Naughton was placed on the full-season injured list, ending his season without appearing in a game.