Parasitic neglected tropical diseases, such as schistosomiasis and soil-transmitted helminthiasis (STH), remain as significant public health concerns in developing countries such as the Philippines. This study aimed to determine the prevalence and intensity of schistosomiasis and STH among school-age children (SAC) and adults in two co-endemic provinces in Mindanao in southern Philippines as part of monitoring of national control programs. Stool samples were collected, processed using Kato-Katz technique, and examined microscopically for presence of intestinal helminth ova. A total of 776 SAC and 526 adults participated in the study. Low schistosomiasis prevalence was generally observed in SAC (0.8%) and adults (0.4%). Generally low STH prevalence was reported in both SAC (3.9%) and adults (3.4%). Only three SAC had heavy intensity STH, which was not seen in adults. Results indicate a state of good morbidity control, which may be a result of effective implementation of mass drug administration (MDA) strategy for schistosomiasis, STH, and lymphatic filariasis in the last several years. The low prevalence and intensities of infections may also be partly attributed to the low diagnostic sensitivity of Kato-Katz technique in detecting low intensity intestinal helminth infections. While results of this study also indicate similarly low levels of both these infections in previous studies, sustaining high MDA coverage rates and addressing remaining challenges related to intensified case finding and treatment, improvements in safe water, sanitation, and hygiene, veterinary public health, and vector ecology and management will be necessary to interrupt transmission in these areas.