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We report a case of neonatal lupus erythematosus (NLE) that presented with systemic cutaneous lesions and thrombocytopenia at birth. A female neonate weighing 1909 g was delivered by cesarean section due to non-reassuring fetal status at 35 weeks of gestation, with recurrent late decelerations and decreased baseline variability. Umbilical arterial pH level was 7.27. The infant exhibited no signs of arrhythmia. Frequent platelet transfusions and intravenous immunoglobulin administration were required. The mother was revealed to be positive for anti-Ro/SSA and anti-La/SSB antibodies, indicating Sjögren’s syndrome. Future pregnancies should be monitored for NLE. This is the first case of NLE presenting with abnormal intrapartum fetal heart rate patterns.