Two experiments were conducted to determine the effects of protease supplementation on degradation of soybean meal (SBM) allergenic proteins (glycinin and β-conglycinin) and gut health of weaned pigs fed soybean meal-based diets. In experiment 1, 2 SBM samples from 2 different sources were subjected to porcine in vitro gastric degradation to determine the effects of protease (at 15,000 U/kg of feedstuff) on degradation of the soybean allergenic proteins. In experiment 2, 48 weaned pigs (body weight = 6.66 kg) were obtained in 2 batches of 24 pigs each. Pigs were individually housed in metabolic crates and fed 4 diets (12 pigs/diet). The diets were corn-based diet with SBM 1 or SBM 2 without or with protease at 15,000 U/kg of diet in 2 × 2 factorial arrangement. Diets were fed for 10 d and pigs were sacrificed on day 10 for measurement of small intestinal histomorphology, permeability of small intestine mounted in Ussing chambers, and serum concentration of pro-inflammatory cytokines. Two SBM sources (SBM 1 and SBM 2) contained 46.9% or 47.7% CP, 14.0% or 14.6% glycinin, and 9.90% or 10.3% β-conglycinin, respectively. Protease and SBM source did not interact on any of the response criteria measured in the current study. Protease supplementation tended to increase (P = 0.069) the in vitro gastric degradation of glycinin. Protease supplementation tended to reduce (P = 0.099) fluorescein isothiocyanate dextran 4,000 Da (which is a marker probe for intestinal permeability) flow in jejunum, and reduced (P = 0.037) serum TNF-α concentration. Protease did not affect small intestinal histomorphology. In conclusion, protease tended to increase gastric degradation of glycinin and reduce gut permeability, and serum concentration of pro-inflammatory cytokines, indicating that the protease used in the current study can be added to SBM-based diets for weanling pigs to improve gut health.