Metaheuristic algorithms have been widely used in determining optimum rational polynomial coefficients (RPCs). By eliminating a number of unnecessary RPCs, these algorithms increase the accuracy of geometric correction of high-resolution satellite images. To this end, these algorithms use ordinary least squares and a number of ground control points (GCPs) to estimate RPCs. Due to the cost of GCP collection, using limited GCPs has become an attractive topic in various research studies. A configuration for RPC estimation using metaheuristic algorithms, namely, discrete-binary configuration for rational function model (DBRFM), is presented to find the optimal number and combination of RPCs in the case of limited GCPs. Based on the fact that the maximum number of RPCs is twice the number of GCPs, the particle/chromosome in the proposed configuration is composed of two binary and discrete parts. This configuration not only is compatible with the nature of the metaheuristic algorithms but also significantly reduces the search space. The proposed method has been tested on various types of remotely sensed data sets. The results of the experiments indicate the superiority of the DBRFM in comparison with the traditional binary configuration of metaheuristic algorithms.