Background Futsal demands lower limb power, repeated sprint ability, and technical prowess. Furthermore, anthropometric characteristics have been shown to influence physical capacities and sports performance and, thus, should be assessed alongside physical fitness levels to maximize performance. Methods This study aimed to investigate the potential correlations between anthropometric characteristics and physical fitness levels among young Portuguese male futsal players and to compare these attributes across two distinct age groups. Twenty-one male athletes from two age groups (Under-18: N=14 - 16.1 ± 0.6 years old; Under-15: N=7 - 13.7 ± 0.6 years old) were recruited to take part in this investigation. Anthropometric characteristics [body weight, height, body mass index (BMI), waist and hip circumference, and waist-to-hip ratio] were assessed, and participants performed three performance tasks (20-meter sprint, vertical and horizontal jump). Results Statistically significant differences regarding body weight (p=0.005), height (p=0.011), and hip circumference (p=0.036) were observed between age groups (Under-18 and Under-15), but no differences were found regarding performance tasks (all p≥0.736). Conclusion After analyzing the entire sample, BMI was found to be inversely correlated with horizontal (r=-0.51; p=0.03) and vertical (r=-0.64; p<0.001) jump performance, and waist-to-hip ratio was positively correlated with 20-meter sprint performance (r=0.70; p<0.001). These indicate a correlation between a higher BMI and waist-to-hip ratio with lower physical fitness levels.