INTRODUCTION: The clivus is an uncommon site for fungal infections and is typically associated with tumors or metastases. Invasive fungal sinusitis extending to the skull base is exceptionally rare and often mimics clival malignancies such as chordomas or metastases. This overlap in clinical and radiological features can lead to diagnostic delays. CASE PRESENTATION: The authors present a case of a 36-year-old immunocompetent male who presented with symptoms and imaging findings suggestive of a malignant skull base tumor, particularly clival chordoma. However, histopathological analysis revealed invasive fungal sinusitis with clival involvement. DISCUSSION: In skull base lesions, particularly those involving the clivus, fungal infections should remain a differential diagnosis, even in patients without immunocompromising conditions. Early diagnosis using biopsy and microbiological analysis is essential for appropriate surgical management and antifungal therapy. CONCLUSION: This case highlights the importance of considering the fungal etiology in clival lesions, especially in high-risk patients. Prompt diagnosis and a multidisciplinary approach can significantly improve the outcomes in rare and complex presentations.