Arterial ischemic stroke (AIS) and cerebral venous sinus thrombosis (CVST) are increasingly recognized as causes of significant childhood disability. Lack of knowledge of the underlying pathogenic mechanisms results in diagnostic challenges and complicates therapeutic decisions, as reflected in divergent recommendations in three sets of pediatric stroke guidelines. In addition, there is a lack of robust evidence from clinical trials to underpin current recommendations regarding evaluation and treatment, in particular relating to antiplatelet therapy, anticoagulation and thrombolysis. With the advent of modern cerebrovascular imaging techniques, the optimal modality for investigating AIS and CVST is subject to debate. The potential role of inflammation in the genesis of arterial disease and the contribution of patent foramen ovale to the etiology of childhood AIS are contentious. Finally, the indications (and optimal technique) for surgical revascularization in children are not established. In this article, we review some of the current concepts and controversies in the investigation and management of AIS and CVST in children.