Microglia are the brain’s resident immune cells, essential for homeostasis and implicated in common neurodegenerative diseases like Alzheimer’s and Parkinson’s disease (PD), where their early activation and sustained inflammatory mediator release precede neuronal loss. By contrast, their contribution to rare disorders is unclear. β-propeller protein-associated neurodegeneration (BPAN), caused by WDR45 mutations, shares key features with PD, including iron accumulation and dopaminergic neuron loss, but the impact of microglia and mutant WDR45 in BPAN remains unexplored. To address this, we established the first iPSC-derived microglia model from BPAN patients and performed secretomics using the hiSPECS method.