Diagnosis of pigmented lesions of the mouth and oral mucosal tissues is challenging. Even though epidemiology may be of some help in orientating the clinician and even though some lesions can be diagnosed on clinical grounds alone, the definitive diagnosis requires histopathological examination. We report a case of pigmented fungiform papillae on the tongue secondary to iron deficiency anaemia. After extensive literature search we found very few cases of pigmented fungiform papillae on the tongue due to iron deficiency anaemia in paediatric population. Hence here we report a 12-year-old male presented with patchy pigmented areas on his tongue of 4 years duration. We gave iron plus folic acid tablets for 6 months with complete disappearance of the lesions.