This study investigated the influence of Bacillus‐based probiotics on performance and intestinal health in broiler challenged with Clostridium perfringens‐induced necrotic enteritis. One‐day‐old Arbor Acre (n = 480) were randomly assigned to four treatments with 10 cages of 12 birds: (a) basal diet negative control (NC), with no probiotics nor antibiotics formulated to contain 2,930 and 3,060 kcal/kg with 24.07 and 15.98% CP, for starter and finisher diet, respectively, (b) basal diet + enramycin (5 mg/kg), an antibiotic growth promoter (AGP); (c) basal diet + Bacillus subtilis B21 at 2 × 109 CFU per g (BS); (d) basal diet + Bacillus licheniformis B26 at 2 × 109 CFU per g (BL); growth performance, intestinal morphology, intestinal lesion scores, short‐chain fatty acids (SCFAs) and mucosal barrier tight junction's (TJ) mRNA expression were assessed. NC‐ and BL‐fed groups showed higher (p = 0.005) average daily feed intake from d1 to d21 than AGP and BS, whereas BS‐ and AGP‐fed groups showed higher average daily weight gain from d22 to d42 and d1 to d42 of age. Higher mortality rate of (12.5%) and lower of (5.5%) were recorded in AGP and NC fed‐groups respectively, lesion score was higher in BS and BL than in AGP, while no lesion was observed in NC group, results revealed higher duodenum and jejunum villus height to crypt depth (VH:CD) compared with NC and BS. Probiotics‐fed groups showed higher total (SCFAs), acetic and butyric acid concentrations at d21 post‐challenge (PC) than other groups. The expression of claudin‐1 was upregulated in duodenum (d7) PC and in jejunum (d7) and (d21) PC in BL group, while at d21 PC, the expression of occludens was higher in jejunum and ileum by AGP and BL. The present study indicated both BS and BL have some similarity with AGP in preventing or partially preventing NE effect in broilers.