In this paper, we propose a numerical approach for solving the nonlinear fractional Klein–Gordon equation (FKGE), a model of significant importance in simulating nonlinear waves in quantum mechanics. Our method combines the Bernoulli wavelet collocation scheme with a functional integration matrix to obtain approximate solutions for the proposed model. Initially, we transform the main problem into a system of algebraic equations, which we solve using the Newton–Raphson method to extract the unknown coefficients and achieve the desired approximate solution. To theoretically validate our method, we conduct a comprehensive convergence analysis, demonstrating its uniform convergence. We perform numerical experiments on various examples with different parameters, presenting the results through tables and figures. Our findings indicate that employing more terms in the utilized techniques enhances accuracy. Furthermore, we compare our approach with existing methods from the literature, showcasing its performance in terms of computational cost, convergence rate, and solution accuracy. These examples illustrate how our techniques yield better approximate solutions for the nonlinear model at a low computational cost, as evidenced by the calculated CPU time and absolute error. Additionally, our method consistently provides better accuracy than other methods from the literature, suggesting its potential for solving more complex problems in physics and other scientific disciplines.