Context: Necrotic enteritis (NE) has been considered a major threat to broiler gut health and growth performance. Aims: This study aimed at investigating the effects of l-arginine (Arg) or l-citrulline (Cit) supplementation on intestinal morphology, short-chain fatty acid (SCFA), microbiota count, gut permeability, and pH in broilers fed reduced-protein diets during subclinical NE challenge. Methods: Ross 308 cockerels (n = 720) were randomly assigned to six experimental treatments with eight replicates of 15 birds per pen. The treatments were standard protein without NE challenge (SP−), or with NE challenge (SP+); reduced protein (two percentage points lower crude protein) without NE challenge (RP−), or with NE challenge (RP+); RP+ plus added Arg (103% of Ross 308 requirement, RPA+) and RPC+ where supplemental Arg in RPA+ was replaced with Cit. A 2 × 2 factorial arrangement was employed for the first four treatments. Factors were NE (− or +) and protein concentration (SP or RP). Treatments SP+, RP+, RPA+, and RPC+ were analysed by one-way ANOVA. Key results: Necrotic enteritis × protein interactions were detected for serum fluorescein isothiocyanate dextran (FITC-d) level, C. perfringens (P < 0.05) count in the caeca (P < 0.01), and acetic acid (P < 0.01) and total SCFA concentrations in the ileum on Day 16 (P < 0.001). Feeding the RP diet reduced serum FITC-d concentration, number of C. perfringens in the caeca, and increased acetic acid and total SCFA concentrations in the ileum compared with the SP group only in birds challenged with NE. Birds in the RPC+ treatment had greater jejunal villus height (P < 0.001), and lower caecal C. perfringens and Enterobacteriaceae count than did those in the SP+ treatment (P ≤ 0.001). Conclusions: The results indicated a benefit to gut health of broilers during NE challenge when replacing crystalline Arg with Cit in RP diets. Implications: In part, replacement of Arg by Cit in the RP diets is of great potential to increase gut health, reduce growth loss, thus, minimising negative effects of NE in broilers.