Kernel methods for solving partial differential equations work coordinate-free on the surface and yield high approximation rates for smooth solutions. Localized Lagrange bases have proven to alleviate the computational complexity of usual kernel methods for data fitting problems, but the efficient numerical solution of the ill-conditioned linear systems of equations arising from kernel-based Galerkin solutions to PDEs is a challenging problem which has not been addressed in the literature so far. In this article we apply the framework of the geometric multigrid method with a τ≥2-cycle to scattered, quasi-uniform point clouds on the surface. We show that the resulting solver can be accelerated by using the Lagrange function decay and obtain satisfying convergence rates by a rigorous analysis. In particular, we show that the computational cost of the linear solver scales log-linear in the degrees of freedom.