Academic achievement is a critical measure of intellectual ability, prompting extensive research into cognitive tasks as potential predictors. Neuroimaging technologies, such as functional near-infrared spectroscopy (fNIRS), offer insights into brain hemodynamics, allowing understanding of the link between cognitive performance and academic achievement. Herein, we explored the association between cognitive tasks and academic achievement by analyzing prefrontal fNIRS signals. A novel quantum annealer (QA) feature selection algorithm was applied to fNIRS data to identify cognitive tasks correlated with CSAT scores. Twelve features (signal mean, median, variance, peak, number of peaks, sum of peaks, range, minimum, kurtosis, skewness, standard deviation, and root mean square) were extracted from fNIRS signals at two time windows (10- and 60-s) to compare results from various feature variable conditions. The feature selection results from the QA-based and XGBoost regressor algorithms were compared to validate the former’s performance. In a two-step validation process using multiple linear regression models, model fitness (adjusted R2) and model prediction error (RMSE) values were calculated. The quantum annealer demonstrated comparable performance to classical machine learning models, and specific cognitive tasks, including verbal fluency, recognition, and the Corsi block tapping task, were correlated with academic achievement. Group analyses revealed stronger associations between Tower of London and N-back tasks with higher CSAT scores. Quantum annealing algorithms have significant potential in feature selection using fNIRS data, and represents a novel research approach. Future studies should explore predictors of academic achievement and cognitive ability.