After his playing career ended, Prothro became an assistant baseball coach at North Iowa Area Community College, where he worked with hitters, catchers and outfielders.
[1] In July, 2015, Prothro was hired as the recruiting coordinator at South Alabama.
[2] On September 30, 2020, Prothro was named the 8th head coach in the history of Eastern Kentucky.
[3] Prothro announced on March 25, 2024, that he was taking a medical leave of absence from EKU effective immediately, with assistant coach Walt Jones serving as the acting head coach during his absence.
[4] On May 15, Prothro announced he will not return to the program and that Jones was named head coach moving forward.