The objective was to compare clinical protection [evaluated through health scoring, endoscopy score of the upper respiratory tract (URT-ES), leukocyte count, viremia, and virus shedding in nasal secretions] following Bovine viral diarrhea virus 2 (BVDV2) and Bovine herpes virus 1 (BHV1) challenge among calves submitted to modified-live virus (MLV) booster vaccination (either intranasal or subcutaneous) concurrent with injectable trace minerals (ITM) or saline. Forty-eight dairy calves received an MLV intranasal (IN) vaccine containing BHV1, BRSV, and BPI3V and subcutaneous (SC) ITM (Se, Cu, Zn & Mn; ITM, n = 24) or saline (SAL, n = 24). Ten weeks later, calves received a second dose of ITM, or saline, according to previous groups and were randomly assigned to receive the same IN vaccine [ITM-IN (n = 12), SAL-IN (n = 12)] or a SC MLV vaccine containing BHV1, BRSV, BPI3V, BVDV1 & 2 [ITM-SC (n = 12), SAL-SC (n = 12)]. Additionally, 12 calves did not receive vaccine or treatment and served as a control group (UNVAC, n = 12). Forty-nine days after booster, calves were challenged with BVDV2; and seven days later with BHV1. Health scores indicated disease in UNVAC on days 6, 10 and 12 compared to the vaccinated groups. Unvaccinated calves had the highest URT-ES after BHV1 challenge. Calves that received SC booster had lower URT-ES after BHV1 challenge than UNVAC calves. Calves in ITM-IN had significantly lower URT-ES after BHV1 infection than SAL-IN and UNVAC calves. In conclusion, IN or SC MLV vaccination was similarly effective in protecting calves from BVDV2 + BHV1 challenges (reducing clinical and endoscopy scores, preventing leukopenia, and viremia), compared to unvaccinated calves. Endoscopic evaluation of the URT allowed visualization of the inflammation and damage at multiple depths in the URT caused by a serial BVDV2 + BHV1 challenge. Calves that received SC vaccination had significantly lower URT-ES after BHV1 challenge than the UNVAC calves. Administration of ITM concurrent with IN vaccination was associated with reduced URT inflammation after BVDV2 + BHV1 challenge.