Cryptococcosis, a rare deep fungal infection, primarily affects immunocompromised individuals and carries a high mortality risk when hematogenously disseminated to the central nervous system (CNS). Cutaneous cryptococcosis poses diagnostic challenges due to its diverse and nonspecific dermatological manifestations. Traditional diagnostic methods, including mycological examination, culture, and histopathology, are time-consuming and require specialized expertise, often leading to misdiagnosis. Metagenomic next-generation sequencing (mNGS), an advanced molecular tool, enables rapid and unbiased pathogen identification. Here, we present the first documented case of cutaneous cryptococcosis diagnosed via mNGS, demonstrating its pivotal role in guiding timely treatment despite negative initial conventional tests.