During the last years the modeling of dynamical phenomena has been advanced by including concepts borrowed from fractional order differential equations. The diffusion process plays an important role not only in heat transfer and fluid flow problems, but also in the modelling of pattern formation that arises in porous media. The modified time-fractional diffusion equation provides a deeper understanding of several dynamic phenomena. The purpose of the paper is to develop an efficient meshless technique for approximating the modified time-fractional diffusion problem formulated in the Riemann–Liouville sense. The temporal discretization is performed by integrating both sides of the modified time-fractional diffusion model. The unconditional stability of the time discretization scheme and the optimal convergence rate are obtained. Then, the spatial derivatives are discretized through a local hybridization of the cubic and Gaussian radial basis function. This hybrid kernel improves the condition of the system matrix. Therefore, the solution of the linear system can be obtained using direct solvers that reduce significantly computational cost. The main idea of the method is to consider the distribution of data points over the local support domain where the number of points is almost constant. Three examples show that the numerical procedure has good accuracy and applicable over complex domains with various node distributions. Numerical results on regular and irregular domains illustrate the accuracy, efficiency and validity of the technique. This paper adopts a local hybrid kernel meshless approach to solve the modified time-fractional diffusion problem. The main results of the research is the numerical technique with non-uniform distribution in irregular grids.