Clostridium perfringens remains a persistent public health challenge, being a leading cause of foodborne intoxications and zoonotic infections. In this study, we systematically searched major academic databases for all eligible studies published up to June 10, 2026, with no restrictions on the publication date. Following the PRISMA guidelines, 23 eligible studies were selected. To stabilize variance (particularly for proportions approaching zero or one hundred), a random-effects model utilizing the Freeman–Tukey double arcsine transformation was employed. Subgroup analyses were conducted to investigate potential variations based on sample type, diagnostic methodology, and study origin. The pooled prevalence of C. perfringens, adjusted via the Freeman–Tukey transformation, was estimated at 18% (95% CI: 12% - 25%). Subgroup analysis indicated that the prevalence was significantly higher in intestinal and fecal samples compared to other sources (p < 0.05). Furthermore, studies employing molecular detection methods (e.g., PCR) reported consistently higher prevalence rates than those using traditional culture techniques. Substantial heterogeneity was observed across studies (I2 > 90%), which was further corroborated by meta-regression analysis showing an inverse relationship between sample size and reported prevalence, suggesting that smaller studies may overestimate the true infection rate. These findings indicate that C. perfringens remains an important foodborne pathogen in Iran. The observed prevalence patterns highlight the need for strengthened surveillance and more standardized detection approaches to support more accurate risk assessment and food safety planning.