Background Serum interleukin-6 (IL-6) has a moderate diagnostic performance in pediatric acute appendicitis (PAA). The evidence regarding its capacity to discern between complicated and uncomplicated PAA is scarce. Methods We designed a prospective observational study to validate serum IL-6 as a marker for diagnostic classification between complicated and uncomplicated PAA. This study included 205 patients divided into three groups: (1) patients who underwent major outpatient surgery (n = 57); (2) patients with non-surgical abdominal pain (NSAP) in whom the diagnosis of PAA was excluded (n = 53), and (3) patients with a confirmed diagnosis of PAA (n = 95). The PAA patients were further classified as uncomplicated or complicated PAA. IL-6 concentration was determined in all patients at diagnosis. Comparative statistical analysis was performed using the Mann-Whitney U test, the Fisher exact test and the Kruskall Wallis test. The area under the receiver operating characteristic curves (AUC) were calculated. Results Median (interquartile range, IQR) serum IL-6 values were 2 pg/mL (2.0-3.4) in group 1, 3.9 pg/mL (2.4-11.9) in group 2, and 23.9 pg/mL (11.1-61.0) in group 3 (P < 0.001). Among the participants in group 3, those with uncomplicated PAA had median (IQR) serum IL-6 values of 17.2 pg/mL (8.5-36.8), and those with complicated PAA had 60.25 pg/mL (27.1-169) serum IL-6 (P < 0.001). At the cut-off point of 19.55 pg/mL, the AUC for the discrimination between patients in group 2 vs. 3 was 0.83 [95% confidence interval (CI) 0.76-0.90], with a sensitivity of 61.3% and a specificity of 86.8. The AUC for the discrimination between patients with uncomplicated and complicated PAA was 0.77 (95% CI 0.68-0.86) and the cut-off point was 25.90 pg/mL, with a sensitivity and specificity of 84.6% and 65.6%, respectively. Conclusions Serum IL-6 has a good performance in discerning between complicated and uncomplicated PAA. A score including clinical and radiological variables may increase the diagnostic performance of this molecule.