Among heterotaxy syndromes, asplenia is often associated with complex congenital heart disease. Asplenia also increases the risk of developing invasive bacterial infections, and recently, prevention has become more important than was earlier thought. The patient, a 7-month-old girl, had undergone abdominal surgery for anal atresia, duodenal obstruction, and Meckel’s diverticulum. She had experienced repetitive infection-related wheezes and then developed coughing, wheezing, and worsening symptoms, so she was urgently admitted with pallor and cyanosis at night. She was treated with inhalational beta-adrenergic agonists and corticosteroids for bronchial asthma, but because her symptoms persisted, she required a high-flow nasal cannula (HFNC). After administering HFNC therapy, her symptoms gradually improved, so she was weaned from HFNC on post-admission day 9 and discharged on day 11. To elucidate the etiology of her wheezing, a computed tomography (CT) scan was performed, which revealed bridging bronchus, bronchial stenosis, and asplenia. Echocardiography and CT revealed an atrial septal defect with a very trivial left–right shunt, right aortic arch, and anomalous origin of the left-subclavian artery. A hemogram on admission revealed Howell Jolly bodies (1％). She was diagnosed with asplenia without complex congenital heart disease and started on antibiotic prophylaxis. This case highlights the importance of understanding that asplenia can manifest in the absence of complex congenital heart disease and require adequate precautions against invasive bacterial infections in patients with asplenia.