The paper addresses the 2D observer-based control of a magnetic microrobot navigating in a cylindrical blood vessel along a reference trajectory. In particular, this robot faces the nonlinear drag force induced by the pulsatile blood flow, which can hardly be measured. We consequently propose a mean value theorem (MVT) based observer to estimate the blood velocity from the sole measurement of the robot position. We also prove the stability of the observer-based backstepping controller. The resulting estimation and tracking are then illustrated through simulations, as well as robustness to parametric uncertainty, measurement noise, and dynamical errors when the pulsatile blood flow is incorrectly modeled.