Introduction: Histiocytic necrotic lymphadenitis (HNL), also known as Kikuchi–Fujimoto disease (KFD), is a rare local lymphadenopathy with a benign course and clinical manifestations such as fever, lymphadenopathy, rash, hepatosplenomegaly, central nervous system (CNS) symptoms, and hemophilic cell syndrome. It was first identified by Japanese pathologists Kikuchi and Fujimoto. KFD damages the meninges, the brain parenchyma, and peripheral nerves in addition to the CNS. Neurological symptoms may even be the most obvious clinical manifestations or initial symptoms of the disease. Case presentation: We present a unique case of a 7-year-old male patient who was diagnosed with activated phosphoinositide 3-kinase delta syndrome 2 (APDS 2) associated with KFD, a HNL during a workup for fever without a focus and cervical lymphadenopathy. Conclusion: Highlighted the unique relationship between two uncommon conditions and stressed the significance of adding KFD to the list of possible diagnoses for lymphadenopathy in APDS 2. Furthermore, we demonstrate that patients with APDS 2 may exhibit low immunoglobulin M levels.