Necrotic enteritis (NE), an enteric disease caused by Clostridium perfringens, and antagonistic effects due to dietary branched-chain amino acid (BCAA) imbalance are key factors that negatively affect chicken growth. The current study was conducted to investigate the effects of valine and isoleucine deficiency in NE challenged broilers. A total of 336 seven-d-old male Cobb 500 were allotted to four treatments with six replicates. The four treatments were as follows: (1) non-challenged control (NC; leucine:lysine = 1.31, valine:lysine = 0.73, and isoleucine:lysine = 0.63), (2) NE-challenged group (NE), (3) NE-challenged with 85 % valine deficiency group (NE-VAL; valine:lysine = 0.62), and (4) NE-challenged with 85 % isoleucine deficiency group (NE-ILE; isoleucine:lysine = 0.54). E. maxima and C. perfringens were administered on d 14 and 18, respectively, and the experiment lasted until d 21. The NE-VAL group had the lowest growth performance measurements compared to the other groups (P < 0.001). All NE-challenged groups had significantly reduced overall growth performance measurements compared to the NC group (P < 0.001). The NE-ILE group showed no difference in any of the measurements compared to the NE group. On d 21, the NE group had significantly increased intestinal permeability, jejunal lesion scores, C. perfringens colony counts, and jejunal chemokine and cytokine gene expression levels, along with decreased intestinal morphology compared to the NC group (P < 0.05). The NE-VAL group had significantly decreased breast muscle yield, reduced lean and total tissue weight, and increased expression levels of mechanistic target of rapamycin pathway and BCAA catabolism-related genes compared to the NE group (P < 0.05). This may explain why the NE-VAL group had the lowest growth performance, as the two negative effects of NE infection and valine deficiency are separated. In conclusion, the negative effects of NE challenge and valine deficiency were independent; valine deficiency showed a similar response to that exhibited by high leucine levels, despite reduced feed intake caused by NE challenge.