Background: Thrombophilia is a prothrombotic disorder that can affect pregnancy outcomes, potentially leading to maternal complications, fetal growth restriction, and adverse perinatal events. However, the precise relationship between thrombophilia and these outcomes remains under investigation, and the impact of hematological, renal, hepatic, and coagulation alterations in thrombophilic pregnancies is not yet fully understood. This study aims to examine the maternal and neonatal consequences of thrombophilia by analyzing key laboratory parameters and perinatal outcomes in affected pregnancies. Methods: A retrospective observational study was conducted on 251 pregnant women, divided into thrombophilic (n = 226) and non-thrombophilic (n = 25) groups. Data on maternal demographics, laboratory parameters (hematological, metabolic, renal, hepatic, and coagulation markers), obstetric outcomes, and neonatal characteristics were extracted from medical records. Statistical analysis included t-tests, chi-square tests, and Pearson correlation analysis to assess the association between thrombophilia and clinical outcomes. Results: Thrombophilic pregnancies were associated with significantly lower fibrinogen levels (p = 0.036) and decreased INR (p = 0.006), suggesting a hypercoagulable state. Renal function was affected, as evidenced by elevated urea (p = 0.012) and creatinine (p = 0.009), indicating a predisposition to kidney dysfunction. Neonates from thrombophilic pregnancies exhibited slightly lower Apgar scores at 1 and 5 min, though the differences were not statistically significant (p = 0.101, p = 0.131). NICU admission rates were comparable between groups (p = 0.317), suggesting that thrombophilia may not be a major determinant of neonatal intensive care needs. However, gestational age and birth weight remained the strongest predictors of neonatal vitality (p < 0.001), while coagulation abnormalities and renal dysfunction correlated with poorer perinatal outcomes. Conclusions: Thrombophilia is associated with altered coagulation profiles, renal dysfunction, and potential risks for maternal complications. While neonatal outcomes were not significantly different, the observed trends suggest the need for enhanced monitoring in thrombophilic pregnancies. Early intervention, thromboprophylaxis, and individualized management strategies may improve maternal and neonatal prognosis. Further research is needed to refine preventive strategies and optimize therapeutic approaches in high-risk pregnancies.