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Septic pulmonary embolism (SPE) is characterised by embolisation of infectious thrombi into the pulmonary circulation and often leads to the formation of nodules and cavities. Although right-sided infective endocarditis (RIE) is a major cause of SPE, reports on the long-term outcomes of pulmonary cavities following SPE remain limited. This report presents the case of a previously healthy early adolescent woman who developed SPE secondary to RIE caused by methicillin-sensitive Staphylococcus aureus. Pulmonary cavities persisted in this patient despite appropriate antibiotic therapy and surgical resection of a vegetation on the tricuspid valve, which attenuated the acute phase of SPE. One year later, chronic pulmonary aspergillosis (CPA) was diagnosed, and oral itraconazole therapy was started. The pulmonary cavities have gradually reduced in size over more than 10 years of follow-up and resolved without surgical intervention.