The optimal feeding time of microencapsulated sodium butyrate (SB) in whole milk (WM) and starter feed on growth performance and health in dairy calves was evaluated. Forty-eight newborn Holstein calves (body weight (BW) = 39.45 ± 2.48 kg) were randomly assigned to one of the four treatment groups (12 calves per treatment; seven females and five males) in a complete randomized block design and fed (1) WM without microencapsulated SB (CON) supplementation; (2) 4 g/day SB added to WM since days 4–32 (SB-4-32); (3) 4 g/day SB added to WM since days 61–74 and an equal amount was added to starter since days 75–88 (SB-61-88) and (4) 4 g/day SB added to WM since days 4–74 and an equal amount was added to starter since days 75–88 (SB-4-88). Total dry matter intake, starter intake, BW, average daily gain and gain-to-feed were similar between treatments. Calves fed SB-4-32, and SB-4-88 had lower faecal score during pre-weaning, and overall. In addition, calves in SB-4-32 and SB-4-88 groups had fewer numbers of days with scours during the pre-weaning period, and throughout the study. Calves fed SB-61-88 had greater serum total protein during post-weaning. Post-weaning and overall albumin concentrations were greater in SB-4-32 and SB-4-88 calves and tended to be greater in the pre-weaning period compared to control calves. In general, the time of SB addition had no remarkable effect on performance but better faecal score within the pre- and post-weaning periods.