Background: Human immunodeficiency virus (HIV) and intestinal parasites co-infections are the most common causes of clinical illness and death, especially for children living in resource constrained setting. Therefore, the aim of this study was to determine the prevalence and associated factors of intestinal parasites among highly active anti-retroviral therapy (HAART) initiated children. Methods: Cross-sectional study was conducted among 255 HAART initiated HIV-infected children at the University of Gondar Comprehensive Specialized Hospital from January to April 2020. Socio-demographic characteristics were collected using a structured questionnaire via a face-to-face interview. Clinical data of the children were collected by reviewing the medical records. Venous blood was collected for complete blood counts, viral load determination, and blood film examination. Flotation concentration technique was done in addition to direct wet mount for parasitological examination. Bi-variable and multi-variable logistic regression analysis were used to check the presence of significant association, and P-value<0.05 was considered as statistically significant. Results: The overall prevalence of intestinal parasite infection (IPI) among the study participants was 22.4% (95% CI=17-28%). The presence of opportunistic infection (AOR=2.09 95% CI=1.81-5.43), no eating under-cooked animal products (AOR=0.38 95% CI=0.16-0.94), male sex (AOR=0.45 95% CI=0.22-0.90), viral load rate >1,000 copies/mL (AOR=1.80 95% CI=1.67-4.19), and cytopenia (AOR=2.71 95% CI=1.59-12.25) showed significant association with the prevalence of IPI. Conclusion: Entamoeba histolytica and Ascaris lumbricoides were the most prevalent intestinal parasites among HAART initiated children. Among HAART initiated children, IPI were associated with gender, cytopenia, viral load, undercooked animal products, and the presence of opportunistic infections. Therefore, health education, prompt treatment, and regular deworming should be implemented to alleviate the burden of intestinal parasites in HIV-infected children.