The generalized finite difference method (GFDM) is a meshless method that has become popular in recent years. The basic theory underlying GFDM is to expand the point cluster function value at the center node by Taylor’s formula and then obtain the best linear combinations of these function values to represent the derivative at the central node by the least square fitting technique. Subsequently, the minimized weighted error between the approximated value and the accurate value is obtained. This paper establishes the general steps for solving waveguide eigenvalue problems with GFDM. Excellent performance is shown by comparing the proposed method and other common solutions. The robustness of the proposed method is verified by calculating the cutoff wavenumbers of typical waveguides and the eccentric circular waveguide in different modes.