Background: Blastocystis sp. is one of the most prevalent parasites found in human stool and has been recently considered an opportunistic emerging pathogen in immunocompromised individuals. However, cases of invasive intestinal infections and skin rashes have been attributed to infection by Blastocystis sp in immunocompetent individuals, suggesting that it is an emerging parasite with pathogenic potential. Findings: We present a case of a 22 year old female patient who complained of pain in the left hypochondrium. Ultrasonography and abdominal computed tomography scans showed two splenic cysts. The cyst fluid analysis demonstrated numerous Blastocystis sp.; PCR and DNA sequencing analyses confirmed the presence of Blastocystis subtype 3. Conclusions: This is, to our knowledge, the first case report of the presence of Blastocystis subtype 3 in extra-intestinal organs and is strong evidence that Blastocystis sp. is potentially pathogenic and invasive. However, further studies are required to determine the pathogenicity of the parasite.