This paper designs a Dirichlet boundary controller to stabilize a heat equation with boundary disturbance within a prescribed finite time independent of initial conditions. We first use boundary measurements and time-varying gain to construct a disturbance estimator that estimates the disturbance itself and the system state within a prescribed time. We then design the estimation-based prescribed time boundary controller by the backstepping transformation with a time-varying kernel. The control gain proposed here diverges as the time approaches the prescribed time. Nevertheless, we can demonstrate the controller’s boundedness and the system’s prescribed time stability. A simulation example illustrates the theoretical result.