Introduction: Hospital-acquired malnutrition (HAM) is prevalent among hospitalised children in developing countries. This condition relates to worse clinical outcomes, prolongs length of stay in hospitals, and increases mortality. A multidisciplinary approach should be performed to prevent and manage this problem. However, HAM is often underdiagnosed, especially in rural hospitals with limited human resources. This study aims to delineate the risk factors of HAM among hospitalised children in a rural hospital. Methods: This nested case-control study derived from the implementation of a nutritional screening programme in Parindu Hospital, Sanggau, West Borneo, was conducted from December 2018 to February 2019. HAM was defined as a loss of body weight of >2% after hospitalisation. Independent variables such as the age of patients, fever, gastrointestinal loss, pre-existing malnutrition, length of stay, and grade of disease were analysed in univariate and multivariate analyses using logistic regression. Risk factors were expressed as odds ratio and adjusted odds ratio (aOR) with 95% confidence interval (CI). Results: Thirty-three patients were analysed as cases with 59 controls. Median age was younger in the case group (49 months, IQR 14-72.5) than control group (88 months, IQR 43-116). After adjustment for other covariates, age <5 years old (aOR 5.50, 95% CI 1.95- 15.59) and moderate-to-severe grade of disease (aOR 3.50, 95% CI 1.09-11.09) were significant risk factors of HAM in our study. Conclusion: Risk factors of HAM in children hospitalised in a rural hospital were age <5 years old and moderate-tosevere grade of disease.