This study was conducted to examine the effects of varying selenium (Se) inclusion levels, in the form of Se-enriched mushroom powder (SeMP) and selenite, on post-weaning growth performance (Period 1; day 1–21), intestinal health and antioxidant capacity (Period 2; day 21–39). Weaned pigs were blocked according to live weight, sex and litter of origin and randomly assigned to the following experimental groups: basal (basal + selenite (0.3 ppm Se)); ZnO (basal + ZnO + selenite (0.3 ppm Se)); 0.15 SeMP (basal + SeMP (0.15 ppm Se)); 0.3 SeMP (basal + SeMP (0.3 ppm Se)) and 0.6 SeMP/Sel (basal + SeMP (0.3 ppm Se) + selenite (Sel) (0.3 ppm Se)) with eight replicates/experimental group. After 21 days, the ZnO experimental group was removed from the experiment and the remaining pigs continued on their respective diet until day 39 post-weaning (Period 2). In Period 1, 0.15 SeMP supplementation reduced (p < 0.05) average daily gain (ADG), average daily feed intake (ADFI) and day 21 body weight, and increased (p < 0.05) faecal scores compared to the ZnO group. Supplementation with 0.3 SeMP and 0.6 SeMP/Sel during Period 1 resulted in similar (p > 0.05) ADG, ADFI, gain-to-feed ratio (G:F) and body weight compared to the ZnO group. However, 0.6 SeMP/Sel supplementation increased (p < 0.05) faecal scores compared to the ZnO group. In Period 2, 0.6 SeMP/Sel increased (p < 0.05) ADG, feed efficiency and day 39 body weight compared to the basal group. Supplementation with Se-enriched mushroom powder, at all inclusion levels, increased (p < 0.05) the abundance of Prevotellaceae and Prevotella, decreased (p < 0.05) the abundance of Sporobacter and increased (p < 0.05) the expression of SELENOP in the jejunum compared to the basal group. Lactobacillaceae and Lactobacillus was increased (p < 0.05) in 0.15 SeMP and 0.3 SeMP pigs compared to the basal group. Selenium deposition in muscle and liver tissue increased (p < 0.001) as a function of inclusion level while pigs supplemented with 0.3 ppm organic Se (0.3 SeMP) had an increase (p < 0.05) in total Se in the muscle compared to pigs supplemented with 0.3 ppm inorganic Se (basal). In conclusion, 0.3 SeMP supplementation led to positive effects on faecal scores and had similar pig performance compared to ZnO in Period 1, while the addition of 0.3 ppm selenite to 0.3 SeMP (0.6 SeMP/Sel) in Period 2 led to enhanced pig performance and aspects of gastrointestinal health.