BACKGROUND: Actinomyces spp. are most commonly found in human commensal flora; however, they have also been shown to cause suppurative infections. We present a case of a rare Actinomyces funkei bacteraemia from an infected deep vein thrombosis in a patient who went on to develop pulmonary cavities secondary to septic emboli. Infected thrombi and septic emboli have been associated with other Actinomyces spp. in the literature, often posing a diagnostic challenge and, in some cases, causing drastic clinical deterioration in patients. The literature regarding Actinomyces funkei is scarce and to our knowledge there are no reports of a relationship between this Actinomyces subspecies and infected thrombi or septic emboli. CASE PRESENTATION: The patient was a 39-year-old known intravenous drug user who presented with a groin injecting site sinus and systemic symptoms. The bacteria was first observed by gram staining of a blood culture sample after 48 h of incubation and the species was identified using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) as Actinomyces funkei. Sputum cytology/histology with cell block revealed a branching gram-positive species suspicious of slow growing bacteria or fungus. CT imaging of his lower limb and chest revealed an extensive DVT with inflammatory changes and pulmonary cavities respectively. The patient was treated with Ceftriaxone before being discharged with a 6-month course of Linezolid. He made a good recovery with reduction in size of the cavitating lung lesions on follow-up imaging. CONCLUSIONS: This case report presents a difficult-to-diagnose bacterial infection in an intravenous drug user, complicated by bacteraemia and secondary septic emboli. Relatively little is known about Actinomyces funkei, and therefore this report aims to increase clinician awareness of diagnosis, management, and complications.