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Introduction Hospital-acquired malnutrition (HAM) is increasingly recognised as an important yet underdiagnosed problem in paediatric inpatient care. Nutritional status can decline quickly during hospitalisation due to illness severity and inadequate intake. However, data on the burden and determinants of HAM in children remain limited particularly in resource-limited settings.Objective This study aimed to determine the prevalence and identify factors associated with malnutrition among hospitalised children.Methods Medical records of children aged 1 month to 15 years admitted to Naresuan University Hospital between 1 January 2019 and 31 December 2020 were reviewed. A total of 368 children met the inclusion criteria. Anthropometric data were collected at admission, 48 hours after admission and discharge. HAM was defined as a decrease in body mass index z-score during hospitalisation. Data were analysed using Stata V.18. Univariate and multivariate logistic regression analyses were performed to identify risk factors, with results expressed as adjusted ORs (aORs) and 95% CIs. A p value <0.05 was considered statistically significant.Results The prevalence of HAM was 6.3%. Univariate analysis showed significant associations with age >12–36 months (OR 0.27; 95% CI 0.09 to 0.81), age >36 months (OR 0.24; 95% CI 0.09 to 0.65), length of hospital stay (LOS) 4–7 days (OR 14.21; 95% CI 3.21 to 62.95), LOS >7 days (OR 14.63; 95% CI 2.73 to 78.49), fever (OR 6.87; 95% CI 2.00 to 23.52) and nosocomial infection (OR 10.86; 95% CI 1.72 to 68.54). Multivariate analysis identified LOS 4–7 days (aOR 8.72; 95% CI 1.77 to 43.09) and LOS >7 days (aOR 9.52; 95% CI 1.46 to 63.13) were independently associated with HAM.Discussion HAM occurred in 6.3% of hospitalised children. Prolonged hospitalisation was the factor most strongly associated with HAM, highlighting the importance of continuous nutritional monitoring and early intervention during inpatient care.