Deep venous thrombosis is a possible complication of indwelling central venous catheters (CVC), with an incidence as high as 61%. We report a case of successful thrombolysis of a CVC-related right atrial thrombus in a pediatric cancer patient with recombinant human tissue plasminogen activator (0.1 mg/kg per h for 12 h) and heparin (10 IU/kg per h for 24 h) administered for 6 days. Daily echocardiographic examination showed progressive lysis of the thrombus. The thrombolytic treatment was associated with mild oozing from the venipuncture sites, but no major bleeding was noted; moreover, thrombin, thromboplastin time and fibrinogen were normal or only minimally altered. Anticoagulant therapy, with or without CVC removal, is the treatment of choice for uncomplicated CVC-related thrombosis. Fibrinolytic therapy may be indicated in some cases at risk of pulmonary embolism or to avoid open heart surgery. Recombinant human tissue plasminogen activator is increasingly used for thrombolytic treatment of organ and limb thrombosis, but experience with it in the pediatric hematology-oncology setting is still limited. This report showed that administering recombinant human tissue plasminogen activator in a pediatric cancer patient prior to hematopoietic stem cell transplantation was effective and safe under strict biochemical and instrumental monitoring. Further studies are needed to determine the best antithrombotic treatment for CVC-related thrombosis, and also the dosage of the medication selected and the duration of treatment.