Nattokinase is a serine protease with fibrinolytic activity and has been proven clinical efficacy and safety for human use by the oral route. In this study, conducted purified recombinant nattokinase from Bacillus subtillis DB104 strain and thrombolytic effects of nattokinase have been observed in vivo. The result of the enzyme purification by membrane filtration method for enzyme recovery efficiency is 82.45%. Then the enzyme was purified to Q-Sepharose ion exchange chromatography with a purification factor of 1.82 and at a yield of 66.91%. Enzyme activity was 5,457 FU/mg protein. With the carrageenan-induced tail thrombosis in a rat model, results were significantly reduced by 67.3 to 83.6% at oral doses and injected nattokinase compared with the control group at 48 h. At 72 hours the rate increased to 82-89% in the oral dose and up to 91% in the injected dose nattokinase and comparable to 90% for heparin-positive hepatitis.