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]
Following two seasons at North Iowa, he joined the coaching staff of the Nicholls State Colonels where he was on the staff of his former head coach at Crowder, Chip Durham.[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.[5]
National champion
Postseason invitational champion
Conference regular season champion
Conference regular season and conference tournament champion
Division regular season champion
Division regular season and conference tournament champion
Conference tournament champion