Objective: Selective serotonin reuptake inhibitors (SSRIs) cross the placenta, and their use during pregnancy can impact neonatal outcomes. However, the effects of maternal SSRI treatment during pregnancy on neonatal urinary and gastrointestinal systems has not yet been investigated. Methods This retrospective case-control study compared neonates born to women who consumed SSRI drugs during pregnancy with the closest birth of healthy delivered newborn not exposed to SSRI in utero, matched for gestational age (GA) and weight for gestational age. The primary outcomes measured were the time to first void and the time to first stool. Results The cohort included 133 neonates in each group. Mothers in the SSRI-exposed group were older (34.5 vs 32.2 years, p<0.001) compared to those in the control group. The time to first stool was significantly shorter in neonates exposed to SSRIs compared to those who were not exposed (7.4 vs 8.6 hours, p=0.023), while the time to first void did not differ between the two groups. In regression analysis, the time to first stool was associated with the time to first void (β=0.138, p=0.032) and SSRI exposure (β=-1.561, p=0.030), but not with GA, gender, and maternal age. SSRI-exposed neonates had three times the rate of formula feeding compared to unexposed neonates (19.5% vs 6%, adjusted p=0.001). Conclusions Maternal SSRI use during pregnancy did not influence the timing of the first void but does impact gut motility.