Cryptococcal meningitis, a severe fungal infection, usually afflicts immunocompromised individuals, mainly those with acquired immunodeficiency syndrome (AIDS). However, rarely, immunocompetent individuals can develop the infection too. Here, we present a case of a human immunodeficiency virus (HIV)-seronegative individual without known immunocompromised states. This patient suffered from chronic headaches for five years before presenting to us, with multiple past consultations resulting in misdiagnoses of migraines and tension-type headaches (TTH). The patient had developed new-onset warning signs in the last month after which neuroimaging was done, which showed features of increased intracranial pressure. Cerebrospinal fluid (CSF) analysis revealed
Cryptococcus neoformans
. The patient received amphotericin B alongside flucytosine, and he underwent three therapeutic lumbar punctures (LP) to relieve symptoms from raised intracranial pressure. Within two weeks, he showed significant improvement in headaches and was discharged in a healthy state. The patient was doing fine two months post discharge. This case emphasizes the necessity of ruling out red flag signs before diagnosing primary headaches. In clinical practice, if any patient shows poor response to medications despite adequate compliance, a thorough evaluation is required to rule out serious causes of headache, with a low threshold for neuroimaging.