Local administration of thrombolytics in ischemic stroke could accelerate clot lysis and the ensuing reperfusion while minimizing the side effects of systemic administration. Medical microrobots could be injected into the bloodstream and magnetically navigated to the clot for administering the drugs directly to the target. The magnetic manipulation that is required to navigate medical microrobots depends on various parameters such as the microrobots size, the blood velocity, and the imposed magnetic field gradients. Numerical simulation was used to study the motion of magnetically controlled microrobots flowing through representative cerebral bifurcations, for predicting the magnetic gradients required to navigate the microrobots from the injection point until the target location. Upon thorough validation of the model against several independent analytical and experimental results, the model was used to generate maps and predictive equations providing quantitative information on the required magnetic gradients, for different scenarios. The developed maps and predictive equations are crucial to inform the design, operation, and optimization of magnetic navigation systems for healthcare applications.