Intestinal helminths are endemic throughout the Philippines; however, there is limited evidence with respect to their prevalence, intensity, and impact on children’s nutritional status. A cross-sectional survey was carried out on 693 children from five rural villages in Northern Samar, the Philippines. Data on dietary intake, nutritional status, and intestinal parasites were collected. Infection with Schistosoma japonicum, Ascaris lumbricoides, Trichuris trichiura, and hookworm was evident in 20.1, 54.4, 71.4, and 25.3% of the children. The majority (84.7%) was infected with one or more helminth species, with about one-quarter of the sample (24.7%) infected with three or more. About half (49.2%, n = 341) of the children were stunted and 27.8% (n = 193) were wasted. A lower prevalence of normal height-for-age (48.3%) appeared in those with polyparasitism, while the prevalence of stunted children increased with infection (46.7% monoparasitism and 51.7% polyparasitism). There was a decreasing trend between infection intensity and the mean values of HAZ and BAZ identified for T. trichiura or hookworm infections. Stunted children were more likely to be male (AOR = 1.58; 95% CI: 1.05–2.39; p = 0.028), older in age (10–14 years) (AOR = 1.93; 95% CI: 1.29–2.88; p = 0.001), and living in poorer households with palm leaves/nipa roof (AOR = 1.85; 95% CI: 1.14–3.01; p = 0.013). Intestinal parasitic treatment needs to be combined with nutrient supplements and health education in order to interrupt the parasite life cycle and achieve sustainable control.