Neonatal aortic thrombosis is a rare occurrence but can be life-threatening. Most aortic thrombosis in neonates is related to umbilical artery catheters. A case of a neonate with a spontaneous aortic thrombosis is described here along with a comprehensive review of the literature for cases of neonatal aortic thrombosis not related to any intravascular device or procedure. The aetiologies of these spontaneous thromboses and the relevance of hypercoagulable disorders are discussed. The cases were analysed for odds of death by treatment method adjusted for era. The reference treatment method was thrombolysis and anticoagulation. No other treatment modality had significantly lower odds than the reference. Surgery alone had higher odds for death than the reference, but this may be confounded by severity of case. The management recommendations for clinicians encountering neonates with spontaneous neonatal aortic thrombosis are discussed.