Thrombolysis is increasingly considered a treatment option in newborns and children with arterial and venous thromboembolic events, or occluded central venous lines. However, no uniform recommendations are available with regard to indications, drug of choice, route of administration, and dosing regimen. Thus, several protocols are used for the different thrombolytic agents, leading to differing outcome with respect to the effectiveness of therapy and bleeding complications. This article will summarize the available information on the use of thrombolytic agents in newborns and children, focussing on the potential indications, efficacy and safety profiles, and evidence supporting dosing schedules.