Background and Aim: We aimed to report newborns with thrombosis and needed fibrinolytic treatment. Patients and methods: This was a retrospective study conducted on 27 newborns with thrombosis followed-up in a neonatal intensive care unit between December 2007 and December 2012. The patients were divided into two groups according to treatment protocol; Group 1 (n=15): recombinant tissue-type plasminogen activator (r-tPA) and Group 2 (n=12): streptokinase (STK). The groups were compared in terms of the efficacy and complications of the treatments. Results: In Group 1, flow restoration was complete in nine (60%) patients, partial in two (13.3%), and absent in four (26.7%). In Group 2, flow restoration was complete in seven (58.3%) patients, partial in three (25%), and absent in two (16.0%). The incidence of complete/partial recovery was similar in the groups. There was no difference between the two groups with regard to the duration of thrombus resolution. Fibrinolytic treatment was terminated in seven patients (46.7%) in Group 1, while in three patients (25%) in Group 2 due to the complications. The most common complications were minor or major bleedings. There was no statistically significant difference with regard to all bleedings complications between the two groups (P=.08), although the incidence of skin hemorrhages was higher in Group 1 (P=.007). There was no significant difference between the mortality rates. Conclusion: Even though the use of STK is not further recommended because of its potential undesirable side effects in newborns, its efficacy and safety appears to be similar to those of r-tPA.