The aim of this study was to evaluate the efficacy of two metaphylactic approaches (long acting antibiotic injected once at 10 days of life or twice at 10 and 35 days of life) on the prevention of bovine respiratory disease (BRD), otitis and mortality in high-risk group-housed pre-weaned Holstein heifer calves. The antibiotic of choice for the metaphylactic approach was a long acting macrolide (tildipirosin) administered subcutaneously at the base of the neck at a dose of 1 mL per 45 kg body weight. A clinical trial was carried out on one dairy farm with random allocation of newborn calves to one of three treatments: (1) control (CTR); (2) one injection at 10 days of life (M1); and (3) two injections at 10 and 35 days of life (M2). Study heifers (n = 795) were reared in group pens of 25 calves per pen and fed unrestricted acidified non-saleable milk from day 1 to day 65 of life. Cox proportional hazard and general linear mixed models were used to evaluate the effect of treatment on mortality, BRD and otitis, and average daily weight gain. The birth weights, proportions of calves with inadequate transfer of passive immunity, proportions of calves born from primiparous dams and proportions of calves born from assisted parturitions were not different among CTR, M1 and M2 treatments. A significantly lower hazard of being affected with BRD and/or otitis (but not for BRD or otitis alone) was observed for M1 (hazard ratio, HR = 0.70, P = 0.009) and M2 (HR = 0.72, P = 0.01) when compared to the CTR group. Metaphylactic treatments had no effect on mortality, otitis and average daily weight gain during the pre-weaning period.