[2][3] The Chicago Cubs selected Thomas in the seventh round of the 2017 MLB draft and he signed, receiving a $175,000 bonus.
In 22 games (twenty starts) between South Bend, Hickory, and the Wood Ducks, Thomas compiled a 3–9 record with a 3.00 ERA over 105 innings.
[8] In 2021, Thomas split the season pitching for the Hickory Crawdads, Double–A Frisco RoughRiders, and Triple–A Round Rock Express, going 3–3 with a 3.66 ERA.
[10] Thomas appeared in 24 games between Double-A Binghamton Rumble Ponies and Triple-A Syracuse Mets where he compiled a 2-0 record and 2.86 ERA with 41 strikeouts in 34.2 innings pitched.
[12] He appeared in 31 games (2 starts) for the Triple–A Salt Lake Bees, compiling a 1-2 record and 5.44 ERA with 45 strikeouts in 44+2⁄3 innings pitched.