After his brother Jeff accepted the head coaching job at Purdue on December 5, 2016, it was rumored that Brohm would be joining Purdue as the co-offensive coordinator/quarterbacks coach. On January 2, 2017, Brian was officially hired at Purdue as an assistant coach. For the 2020 season opener against Iowa, Brohm took over as acting head coach and play-caller after Jeff tested positive for COVID-19, a game that Purdue won 24–20. When Jeff left to become the head football coach at Louisville, Brian was named the interim head coach for Purdue for the 2023 Citrus Bowl.
