Background: The role of Enterobius vermicularis infestation in the context of appendicitis is largely overlooked, but Enterobius vermicularis is considered an unexpected and significant appendicectomy finding. The aim of this study was to investigate the frequency of Enterobius vermicularis findings in appendectomies and to evaluate the clinical and histopathologic features of patients with Enterobius vermicularis-associated acute appendicitis and those with appendiceal Enterobius vermicularis infestation. Methods: The medical records of all children who underwent an appendectomy in two large pediatric centers in Croatia between 1 January 2009 and 1 January 2024 were retrospectively reviewed. Of 6359 appendectomies, 61 (0.96%) children were diagnosed with Enterobius vermicularis on histopathology and included in further analysis. The groups were compared with regard to demographic characteristics, laboratory values, clinical features and histopathological findings. Results: The incidence of enterobiasis fluctuated slightly in the individual study years, but was constant overall. The median age of all patients was 11 years (IQR 8.5, 13), with females predominating (60.7%). Acute appendicitis was observed in 34% of the appendiceal species. The patients with Enterobius vermicularis infestation, without appendicitis, were younger (9 years (IQR 8, 13) vs. 12 years (IQR 10, 15); p = 0.020), had longer duration of symptoms (36 h (IQR, 12, 48) vs. 24 h (IQR, 12, 36); p = 0.034), lower body temperature (37 °C (IQR 36.8, 37.4) vs. 37.6 °C (IQR, 37, 38.6) p = 0.012), lower Appendicitis Inflammation Response (AIR) score (3 (IQR 2, 5) vs. 7 (IQR 5, 9.5) p < 0.001), lower incidence of rebound tenderness (57.1% vs. 20%; p = 0.003) and less frequent vomiting (12.5% vs. 47.6%; p = 0.004) compared to the patients with Enterobius vermicularis-associated acute appendicitis. Acute inflammatory markers in the laboratory showed significantly higher values in the group of patients with acute appendicitis: C-reactive protein (p = 0.009), White blood cells (p = 0.001) and neutrophils (p < 0.001). Eosinophilia was not found in any of the groups, although eosinophil counts were significantly higher in children who had Enterobius vermicularis infestation than in those with Enterobius vermicularis-related appendicitis (2.5% (IQR 0.9, 4.3) vs. 1.8% (IQR 0.7, 2.1); p = 0.040). Conclusions: Pediatric surgeons should consider Enterobius vermicularis infestation as a differential diagnosis when removing a vermiform appendix. Younger age, longer duration of symptoms, lower body temperature, lower AIR score, lower diameter of the appendix and normal laboratory inflammatory markers could predict Enterobius vermicularis infection in children presenting with right iliac fossa pain and avoid unnecessary appendectomy.