Aortic arch thrombosis is an extremely rare but life-threatening diagnosis that is often misdiagnosed in the neonatal period. Strategies including surgical intervention, systemic anticoagulation, and thrombolysis have been previously described in the treatment of these neonates. We describe the case of a neonate who presented with concern for interrupted aortic arch and was diagnosed with an in utero aortic arch thrombosis. To our knowledge, this is the first reported case with evidence of aortic arch thrombosis in fetal life. The patient underwent successful treatment with systemic thrombolysis with tissue plasminogen activator. A brief review of the literature regarding the diagnosis, treatment, and management of neonatal aortic arch thrombosis is also presented.