Superficial fungal infection is quite common in oral cavity and they are completely microbe-oriented disease whereas deep-seated fungal infections are rare. These lesions are often non-specific and could present with a wide array of clinical appearances, ranged from a flat lesion to elevated borders mimicking malignancy-like lesion. This uncertainty pose a challenge in the diagnosis of deep-seated fungal infection . A case report of a 65 year old, former smoker with underlying type II diabetic mellitus, referred to Oral & Maxillofacial Surgery Department for management of a painful lesion on the tongue for 2 weeks. He had no history of blunt trauma. The lesion appeared as sudden onset swelling with raised ulcerated border associated with yellowish slough tissue, measuring about 1.2cm x 1.6cm at the posterior one third at the dorsal surface of the tongue. Nystatin mouthwash 500 000 International Unit was given to rule out median rhomboid glossitis. After 1 week review, he had experienced dysphagia and claim the lesion grew in size. Therefore, nystatin mouthwash was withheld. The patient was prescribed with a course of antibiotics considering superimposed infection. The following week, it was noted the size of the ulcerative lesion increased and pain worsened. Hence, an incisional biopsy of the lesion was performed and histopathology reported as traumatic eosinophilic ulcer. Patient was treated with 0.2 percent hyaluronic acid topical gel, however the lesión did not improve. Based on the progression of the lesión, we decided with second incisional biopsy. Further assessment done by Otorhinolaryngology Department revealed the lesión did not extend to the base of the tongue and blood investigation appeared insignificant. Case was consulted with Oral Pathology and Oral Medicine Specialist and had suggested to start Fluconazole 100 milligram in consideration of deep-seated fungal infection. Despite histopathology reported as pyogenic granuloma, his condition remarkably improved after one week. In conclusión, adequate specimen plays a significant role which is crucially important in facilitating further laboratory investigation by Oral Pathology and Oral Medicine specialist. Therefore, deep-seated fungal infections in the area of oral and maxillofacial región are challenging. One has to differentiate between a mere oral infection and deep-seated fungal infection in order to determine clinical management of the lesión.