Serotonin (5-HT) is a key neuromodulator essential for fetal brain development. In mice, the placenta remains the main source for the fetal cortex until GD 16.5. Maternal conditions that alter serotonin availability during this window may affect neurodevelopment. Our previous work showed that prenatal 5-HT disruption modifies expression of genes encoding the serotonin transporter (SERT) and tryptophan hydroxylase 2 (Tph2)—the enzyme for serotonin synthesis in the CNS—in the medial prefrontal cortex and leads to persistent social behavior deficits. This study aimed to analyze the effects of prenatal serotonin depletion on gene expression and placental structure. Pregnant C57BL/6 mice received a 5-HT synthesis inhibitor (PCPA) or vehicle from GD 12.5 to 14.5. Forty-eight hours after the final injection, cesarean sections were performed. RT-PCR was used to quantify SERT and Tph2 expression in embryonic brains and placentas. Histological analysis (Hematoxylin/Eosin) was performed on placental tissue. Results showed reduced SERT expression in embryonic brains of PCPA-treated animals, with females showing a trend toward increased Tph2 expression. In placentas, SERT expression was decreased, along with morphometric and vascular alterations. These findings suggest that acute prenatal serotonin depletion disrupts gene expression and placental architecture, potentially contributing to long-term behavioral outcomes.