Hypoxaemia in isolated right ventricular (RV) hypoplasia (IRVH) is primarily caused by a right-to-left shunt (RLS) at the atrial level, such as an atrial septal defect (ASD). When considering closure of the RLS, it should be closed only after ensuring that it will not cause right-sided heart failure (HF). A 21-year-old woman had been experiencing shortness of breath during exertion since childhood. Transthoracic and transoesophageal echocardiography revealed an ASD with bidirectional shunting, and microbubble test revealed a marked RLS. Cardiac magnetic resonance imaging revealed a hypoplastic RV end-diastolic volume corrected for body surface area of 47 mL/m2 (70% of normal range). Right heart catheterization revealed a decreased Qp/Qs ratio of 0.89 and a pressure waveform with a clear increase in the 'A'-wave, although the mean right atrial pressure was not high (4 mmHg). Therefore, the patient was diagnosed with cyanotic ASD and IRVH. A temporary balloon occlusion test was performed to evaluate the right-sided heart response to capacitive loading prior to ASD closure. After treatment, the patient's improved markedly. The pre-operative brain natriuretic peptide (BNP) level was normal; however, 6 months after ASD closure, the BNP level was elevated, and the continuous-wave Doppler waveform of pulmonary regurgitation at the time of transthoracic echocardiography changed, suggesting an increase in diastolic RV pressure. When ASD is complicated by hypoxaemia, the possibility of IRVH, although rare, should be considered. Another difficult point is determining whether the ASD can be closed, considering its immature RV compliance.