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Objectives To assess population-level trends in malnutrition among Rohingya refugee children in Cox’s Bazar, Bangladesh, from 2017 to 2024, and examine associations with age, sex, seasonality and food assistance purchasing power.Design A retrospective repeated cross-sectional study analysing anthropometric and economic data from 2017 to 2024.Setting Two primary health clinics in the Kutupalong and Balukhali refugee camps in Cox’s Bazar, home to over one million Rohingya refugees including over 440 000 children facing ongoing food insecurity and limited healthcare access.Participants 13 219 refugee children aged 6–60 months with recorded weight-for-height z-scores (WFZ) and mid-upper arm circumference (MUAC) data in electronic health records. The majority (>80%) of the data were from routine, non-illness-related visits.Main outcome measures Prevalence and severity of global acute malnutrition (GAM), measured by first-visit WFZ and MUAC. Secondary outcomes included seasonal variation, sex and age disparities and trends in e-voucher purchasing power.Results From 2017 to 2024, population-level trends in GAM prevalence significantly increased, peaking at 38.4% in 2021. Male children showed poorer nutritional outcomes (mean WFZ: −0.96 vs −0.89 for females; p=0.005), and malnutrition severity rose with age (p<0.0001). Seasonal nutritional declines occurred during monsoon months, particularly among children aged 25–36 months, independent of infectious disease trends. E-voucher purchasing power declined significantly over time due to inflation, correlating with declining WFZ scores (p<0.0001). Agreement between WFZ and MUAC was limited, indicating measurement method discrepancies.Conclusions Child malnutrition in the Rohingya refugee population remains above WHO emergency thresholds for GAM (15% or higher) despite ongoing aid. Economic inflation was associated with challenges in food assistance, with relatively greater nutritional risk observed among males and children aged 25–36 and 37–60 months. Seasonal vulnerabilities exacerbate risks during monsoons. Policy responses must adjust food assistance for inflation, prioritise age-specific and gender-sensitive nutritional strategies, and strengthen seasonal preparedness.