San Francisco Giants

Kilian spent his first professional season in 2019 with the rookie–level Arizona League Giants and Low–A Salem-Keizer Volcanoes and did not allow an earned run over 16 innings. He did not play in a game in 2020 due to the cancellation of the minor league season because of the COVID-19 pandemic.^[3] Kilian started 2021 with the High–A Eugene Emeralds before being promoted to the Double–A Richmond Flying Squirrels.^[4]

Chicago Cubs

On July 30, 2021, the San Francisco Giants traded Kilian and Alexander Canario to the Chicago Cubs for Kris Bryant.^[5] He was assigned to play for the Tennessee Smokies, but missed the final month of the 2021 season due to injury. Over 19 starts between Eugene, Richmond, and Tennessee, he went 7-4 with a 2.42 ERA and 112 strikeouts over 100+1⁄3 innings.^[6] After the season, Kilian played for the Mesa Solar Sox in the Arizona Fall League. He won the AFL Championship Game's MVP Award after throwing six perfect innings, retiring all 18 batters he faced.^[7] He opened the 2022 season with the Iowa Cubs.^[8]

On June 4, 2022, Kilian was selected to the 40-man roster and promoted to the major leagues for the first time to start against the St. Louis Cardinals.^[9] He made 3 starts for Chicago in his rookie campaign, struggling to an 0-2 record and 10.32 ERA with 9 strikeouts in 11+1⁄3 innings pitched.

Kilian was optioned to Triple-A Iowa to begin the 2023 season.^[10] He made three appearances for the big–league club, struggling to a 16.88 ERA with 5 strikeouts across 5+1⁄3 innings of work.

During spring training in 2024, Kilian strained his teres major muscle and missed the first months of the season.^[11] He was activated from the injured list on July 31.^[12] In 2 games (1 start) for the Cubs, Kilian posted an 0-1 record and 4.22 ERA with 7 strikeouts across 10+2⁄3 innings pitched.

Kilian was optioned to Triple-A Iowa to begin the 2025 season.^[13] After one start for Iowa, Kilian was designated for assignment by Chicago on April 10, 2025.^[14] He was released by the Cubs organization on April 13.^[15] Kilian re-signed with Chicago on a minor league contract on April 16.^[16] He made 11 appearances (one start) for South Bend and Iowa, accumulating a 1-1 record and 7.47 ERA with 14 strikeouts across 15+2⁄3 innings pitched. Kilian elected free agency following the season on November 6.^[17]

San Francisco Giants (second stint)

On December 14, 2025, Kilian signed a minor league contract with the San Francisco Giants.^[18] On March 25, 2026, the Giants selected Kilian's contract after he made the team's Opening Day roster.^[19]