Considering the ever-growing demand for an efficient method of deductive mining and extrapolative analysis of large-scale dimensional datasets, it is very critical to explore advanced machine learning models and algorithms that can reliably meet the demands of modern cellular networks, satisfying computational efficiency and high precision requirements. One non-parametric supervised machine learning model that finds useful applications in cellular networks is the Gaussian process regression (GPR). The GPR model holds a key controlling kernel function whose hyperparameters can be tuned to enhance its supervised predictive learning and adaptive modeling capabilities. In this paper, the limited-memory Broyden–Fletcher–Goldfarb–Shanno (LBFGS) with kernel parameters selection (KPS) algorithm is employed to tune the GPR model kernel hyperparameters rather than using the standard Bayesian optimization (BOP), which is computationally expensive and does not guarantee substantive precision accuracy in the extrapolative analysis of a large-scale dimensional dataset. In particular, the hybrid GPR–LBFGS is exploited for adaptive optimal extrapolative learning and estimation of throughput data obtained from an operational 5G new radio network. The extrapolative learning accuracy of the proposed GPR–LBFGS with the KPS algorithm was analyzed and compared using standard performance metrics such as the mean absolute error, mean percentage error, root mean square error and correlation coefficient. Generally, results revealed that the GPR model combined with the LBFGS kernel hyperparameter selection is superior to the Bayesian hyperparameter selection method. Specifically, at a 25 m distance, the proposed GPR–LBFGS with the KPS method attained 0.16 MAE accuracy in throughput data prediction. In contrast, the other methods attained 46.06 and 53.68 MAE accuracies. Similarly, at 50 m, 75 m, 100 m, and 160 m measurement distances, the proposed method attained 0.24, 0.18, 0.25, and 0.11 MAE accuracies, respectively, in throughput data prediction, while the two standard methods attained 47.46, 49.93, 29.80, 53.92 and 47.61, 52.54, 53.43, 54.97, respectively. Overall, the GPR–LBFGS with the KPS method would find valuable applications in 5G and beyond 5 G wireless communication systems.