Numerical methods for solving differential equations often rely on the expansion of the approximate solution using basis functions. The choice of an appropriate basis function plays a crucial role in enhancing the accuracy of the solution. In this study, our aim is to develop algorithms that can identify an optimal basis function for any given differential equation. To achieve this, we explore fractional rational Jacobi functions as a versatile basis, incorporating hyperparameters related to rational mappings, Jacobi polynomial parameters, and fractional components. Our research develops hyperparameter optimization algorithms, including parallel grid search, parallel random search, Bayesian optimization, and parallel genetic algorithms. To evaluate the impact of each hyperparameter on the accuracy of the solution, we analyze two benchmark problems on a semi‐infinite domain: Volterra's population model and Kidder's equation. We achieve improved convergence and accuracy by judiciously constraining the ranges of the hyperparameters through a combination of random search and genetic algorithms. Notably, our findings demonstrate that the genetic algorithm consistently outperforms other approaches, yielding superior hyperparameter values that significantly enhance the quality of the solution, surpassing state‐of‐the‐art results.