Effect of timing of xylanase supplementation to weanling pigs and its effect on growth performance, nutrient digestibility, and fecal microbiota was investigated. A total of 128 weanling pigs [(Hampshire × Duroc) × (Yorkshire × Landrace); 6.2 ± 0.6 kg body weight (BW); weaning age: 21 d] were assigned to four treatments, with eight replicate pens and four pigs per pen. Treatments were a combination of two dietary treatments (without or with xylanase) in two periods; (period 1, days 0–14) and period 2 (days 14–42): xylanase–xylanase, xylanase–control, control–xylanase, and control–control. Fecal microbiota diversity and apparent total tract digestibility (ATTD) were determined. From days 0–14, pigs had lower (P < 0.01) BW, average daily gain (ADG), and feed efficiency when xylanase was included in the diets. The final BW (P < 0.05) and overall ADG (P < 0.02) at day 42 were greater when xylanase was supplemented from day 14 compared with supplementation from day 0. The apparent ileal digestibility and ATTD of dry matter, gross energy, nitrogen, and phosphorus were increased (P < 0.05) by xylanase. Xylanase significantly decreased (P < 0.05) the relative abundance of Veillonella spp. and tended (P = 0.08) to decrease the relative abundance of Megasphaera spp. in period 2 compared with the non-supplemented group.