Intestinal parasitic infections remain a major cause of morbidity among children in developing countries. This cross-sectional study was to determine the prevalence, species distribution, diagnostic agreement between two microscopy techniques, and risk factors for intestinal parasitic infection among children aged 1–9 years attending Chukwuemeka Odumegwu Ojukwu University Teaching Hospital (COOUTH), Awka, Anambra State, Nigeria, over a six-month period. Stool specimens from 360 children were examined using saline wet mount and formol-ether concentration techniques, and a structured pretested questionnaire captured socio-demographic and environmental risk factors. From the 360 specimens, 134 (37.2%) were positive for at least one parasitic agent. Ascaris lumbricoides dominated (81.3% of positive findings), followed by Trichuris trichiura (9.7%), Entamoeba histolytica (8.2%), and Giardia lamblia (0.7%). The two diagnostic techniques showed substantial agreement (Cohen's Kappa = 0.799; observed agreement = 91.1%), but McNemar's test revealed a significant asymmetry (p = 0.0001), formol-ether concentration detected 27 cases missed by wet mount, compared with only 5 detected by wet mount alone, giving wet mount a sensitivity of 79.1% relative to formol-ether. On multivariate logistic regression, rural residence was independently associated with parasitic infection (adjusted OR = 1.96, 95% CI: 1.18–3.23, p = 0.009), while use of bottled drinking water was protective relative to borehole water (adjusted OR = 0.40, 95% CI: 0.19–0.82, p = 0.012). These findings demonstrate a substantial burden of intestinal parasitic infection among children attending COOUTH, dominated by Ascaris lumbricoides, and confirm that reliance on wet mount microscopy may lead to clinical under diagnosis. Incorporation of a concentration technique and saline wet mount alongside targeted water, sanitation and hygiene interventions in rural communities is recommended.