Given the increased risk of malnutrition in children with cleft lip and/or palate (CLP), determining their nutritional status is critical for preventing adverse surgical risks. However, no such disaggregated, national-level data are available in Indonesia. We aimed to determine the nutritional status of patients with clefts in Indonesia and to identify problems and solutions for malnutrition cases within the population. In this cross-sectional study, we considered records of individuals who underwent primary surgery for CLP in Smile Train-sponsored facilities in Indonesia between 1 January 2016 and 31 December 2021 (n = 18 480). We only included children under the age of five with an evaluation date prior to admission date and excluded subjects with invalid data values. We classified their nutritional status by z-scores according to the World Health Organization Child Growth Standard (2006). Malnutrition cases cover four indicators - stunting, wasting, underweight, and overweight. We compared the prevalence for malnutrition cases in children under the age of five using national health survey data. We included 1899 records following data validation. The national prevalence of stunting (24.4%), wasting (12.5%), and overweight cases (12.9%) was high, while underweight cases (6.8%) were comparatively low. Statistical analyses showed significant differences in nutritional status based on length/height-for-age between girls and boys aged 0-5 months (P = 0.008) and 48-60 months (P = 0.001), and based on body mass index-for-age (P = 0.000) between girls and boys aged 0-5 months. Girls in different age groups exhibited a statistically significant difference in nutritional status based on length/height-for-age (P = 0.002) and weight-for-age (P = 0.017). Concurrent stunting and overweight were the most common forms of concurrent malnutrition (8.7%). We found a significant difference in the prevalence of underweight (P = 0.001) and overweight (P = 0.000) cases between children with CLP and those without CLP. Our findings highlight the importance of nutritional interventions for children with orofacial clefts in Indonesia, and the importance of age and gender in their design and implementation. Further investigation is necessary to explore the risks of overweight and concurrent malnutrition among this population.