The primary cause of branchio-oto-renal syndrome (BORS) is mutations in the EYA1 gene. This study aimed to explore the impact and underlying mechanisms of EYA1 mutations on podocyte injury. We collected clinical and genetic data from a 4-year-old girl diagnosed with BORS and her family. Induced pluripotent stem cells (iPSC) were derived from peripheral blood mononuclear cells of both the patient and healthy individuals, which were differentiated into podocytes in vitro. RNA-seq was used to analyze differentially expressed genes in both groups. Here, the proband, along with his brother and mother, exhibited symptoms of BORS. WES analysis identified a heterozygous splicing variant at the EYA1 locus: c.1050 + 5G > A, inherited from his mother. The proband was initially glucocorticoid-resistant. After tacrolimus treatment, his urine protein/creatinine ratio significantly improved. Compared to healthy individuals, patient-derived podocytes displayed increased motility and pronounced cytoskeletal rearrangement. Dexamethasone was ineffective in ameliorating the pathological damage induced by puromycin aminonucleoside in patient-derived podocytes. RNA-Seq results indicated significant downregulation of cell adhesion molecule signaling pathway expression in patient-derived podocytes compared to healthy controls. In BORS patients with EYA1 mutations, podocytes exhibit cytoskeletal reorganization and enhanced motility in vitro while showing resistance to steroid treatment-indicating a unique damage response that warrants further investigation.