Numerical analysis was performed on the enzyme transport and the flow fields in order to predict the effectiveness of forced injection in thrombolytic therapy. The species and momentum transport equations were numerically solved for the case of uniform perfusion of enzyme into the fibrin clot, and the validity of our methods were verified. In order to predict the lysis efficiency of continuous and forced intermittent injections, enzyme perfusion and clot lysis were simulated for the different injection velocities and frequencies. Intermittent injection showed faster clot lysis compared to continuous perfusion, and lysis efficiency was increased as the injection velocity and period increased.