Abstract Background In Cox's Bazar, Bangladesh, 860 356 Rohingya living in refugee camps have experienced decades of persecution. Little is known about disease burden in this population. Methods A retrospective review of deidentified electronic health records (EHR) of 51 270 Rohingya attending two primary health clinics in Kutupalong and Balukahli from October 2017 to October 2019 was performed. A novel EHR system named NIROG was used for patients' medical records'. Results Females comprised 53.8% of patients. The median age of females was 25 y and for males it was 19 y. Prevalence of adult hypertension and diabetes was 14.1% and 11.0%, respectively. Also, 16.6% of children aged <5 y had moderate or severe acute malnutrition, while 36.6% were at risk of malnutrition. Body mass index (BMI) analysis showed that 34.4% of adults were underweight. Females were more likely to be hypertensive, diabetic, overweight/obese and malnourished. BMI had a statistically significant positive correlation with fasting blood glucose levels and systolic blood pressure. Conclusions The use of a portable EHR system was highly effective at providing longitudinal care in a humanitarian setting. Significant proportions of the adult population appear to have hypertension or diabetes, pointing to a critical need for management of chronic non-communicable diseases (NCDs). The findings of the current study will help stakeholders to plan effective prevention and management of NCDs among displaced Rohingya and other displaced populations.