Background: Cardiac myxoma is the most common primary cancer of the heart in adults. It is characterised by non-specific clinical symptoms and radiological findings. The aim of this study is to present the case of a 3.5-year-old boy diagnosed with right atrial myxoma briefly after the onset of inflammatory bowel disease treatment. Case report: The patient was hospitalised because of chronic diarrhoea, dyselectrolytaemia, and severe cachexia. Following multiple examinations, a diagnosis of inflammatory bowel disease was made. Additionally, due to upper limb oedema, a cardiac consultation and echocardiography were conducted, revealing a solid mass in the right atrium. Consequently, a cardiac surgical intervention was carried out due to the patient’s condition. Conclusions: Right atrial myxomas are extremely rare in paediatric patients, and the coexistence of inflammatory bowel disease and cardiac myxoma has not been previously reported in the literature. Further research is needed to establish the potential correlation between these two diseases.