Carrillo began his professional career with the Single-A Lake Elsinore Storm where he started 7 games and went 1–2 with a 7.01 ERA with 29 strikeouts in 25.2 innings pitched. He then made his way up to Double-A Mobile where he went 1–3 with a 3.02 ERA to go along with 43 strikeouts in 50.2 innings pitched. On May 19, Carrillo joined the Triple-A Portland Beavers. However, he was only able to pitch 2.2 innings because of tightness in his right throwing elbow. Carrillo was sent to the Padre team specialist in San Diego and was told that he would need to rehab the elbow for roughly a month. Carrillo, as well as the Padre organization, were pleased with this as opposed to Carrillo being forced to have surgery.