Isolated sphenoid fungal sinusitis (ISFS) is a rare condition characterized by fungal infection of the sphenoid sinus. It often presents with non-specific symptoms, which can lead to misdiagnosis. This study presents two unique cases of ISFS with mucocele that were initially misdiagnosed as chordoma based on preoperative radiographic findings. Two cases of ISFS were thoroughly investigated, including clinical examinations, radiological assessments, and surgical explorations. The patients’ symptoms, radiographic findings, surgical procedures, and postoperative outcomes were documented. In both cases, radiographic assessments raised suspicion of chordoma due to bony destruction and soft tissue lesions involving the sphenoid sinus and clivus. However, endoscopic sinus surgery revealed fungal balls and mucoceles, confirming the diagnosis of ISFS. Postoperative pathology confirmed the presence of aspergilloma. The patients recovered well with appropriate treatment. ISFS is challenging to diagnose due to its deep anatomical location and non-specific symptoms. Visual disturbances, particularly affecting the abducens nerve, are common. Sphenoid sinus mucocele, though rare, can be present. Surgical exploration plays a crucial role in establishing an accurate diagnosis and initiating appropriate treatment. ISFS can mimic other skull base lesions, such as chordoma, on preoperative radiography. These cases underscore the value of surgical exploration in reaching an accurate diagnosis and highlight the need for the cautious interpretation of radiological findings in sphenoid sinus lesions to ensure optimal patient care.