Background Enteric pathogens contribute to child malnutrition in low-to-middle-income countries. In Timor-Leste, there has been limited study of this relationship. Methodology/Principal findings We investigated enteric disease, stunting, and malnutrition in children in Dili, Timor-Leste (July 2019 – October 2020). Sixty infants received up to four home visits. We collected faecal samples, demographics, anthropometrics, food and water sources, feeding practices, and animal husbandry details. For 160 children admitted to Hospital Nacional Guido Valadares with clinical diagnosis of severe diarrhoea or severe acute malnutrition (SAM), we collected faecal samples, diagnostics, and anthropometrics. Faeces were tested by polymerase chain reaction (PCR) using the BioFire® FilmArray® Gastrointestinal Panel. Descriptive analyses and regression analyses were conducted using R. We detected enteric pathogens in 68.8% (95% confidence interval [CI] 60.4–76.2%) of infants, 88.6% of children with SAM (95% CI 81.7–93.3%), and 93.8% of children with severe diarrhoea (95% CI 67.7–99.7%). Diarrhoeagenic Escherichia coli and Campylobacter spp. were most frequently detected. A median weight-for-height Z-score (WHZ) of -1.1 (interquartile range [IQR] -2.0 to -0.1) for infants across all home visits, -3.9 (IQR -4.7 to -3.0) for children with SAM and -2.6 (IQR -4.2 to -1.1) for children with severe diarrhoea was observed. The most common admission diagnosis was SAM (88.1%, 95% CI 81.7–92.5%). Hospitalised children had increased odds of Shigella/enteroinvasive E. coli (OR 11.4, 95% CI 2.8–47.3) and Giardia lamblia detection (OR 31.7, 95% CI 3.6–280) compared with infants. For home visits, bottle feeding was associated with increased odds of pathogen detection (OR 8.2, 95% CI 1.1–59.7). Conclusions/Significance We detected high prevalence of enteric pathogens and signs of malnutrition in children in Dili. Our pilot is proof of concept for a study to fully explore the risk factors and associations between enteric pathogens and malnutrition in Timor-Leste.