Cryptococcal infection in Nigeria’s advanced HIV disease (AHD) population is not uncommon but is sparsely reported in children. The dearth of data on cryptococcal disease in our paediatric population suggests it is an uncommon clinical entity and may cause delayed diagnosis and preventable deaths. It is pertinent that cognizance be done of this clinical entity in our paediatric population. We report a 16-month-old HIV-positive child with complaints of weight loss of 3 months, cough of 1 month, fever, passage of watery stool, fast and difficulty in breathing for 1 week. She was initially managed as a case of paediatric AIDS with septicaemia and was receiving ceftriaxone and cotrimoxazole. The diagnosis was subsequently reviewed to paediatric AIDS with cryptococcal disease as the cryptococcal antigen screening test was positive and oral fluconazole commenced. However, the patient deteriorated and eventually died. This case report suggests a significant knowledge gap in the occurrence of cryptococcosis in our paediatric population and as a matter of urgency the need to conduct studies targeted at ascertaining the burden of cryptococcosis in children living with AHD in Nigeria.