Objective: This paper presents a graph signal processing (GSP)-based approach for decoding two-class motor imagery EEG data via deriving task-specific discriminative features. Methods: First, a graph learning (GL) method is used to learn subject-specific graphs from EEG signals. Second, by diagonalizing the normalized Laplacian matrix of each subject graph, an orthonormal basis is obtained using which the graph Fourier transform (GFT) of the EEG signals is computed. Third, the GFT coefficients are mapped into a discriminative subspace for differentiating two class data using a projection matrix obtained by the Fukunaga-Koontz transform (FKT). Finally, an SVM classifier is trained and tested on the variance of the resulting features to differentiate motor imagery classes. Results: The proposed method is evaluated on Dataset IVa of the BCI Competition III and its performance is compared to i) using features extracted on a graph constructed by Pearson correlation coefficients and ii) three state-of-the-art alternative methods. Conclusion: Experimental results indicate the superiority of the proposed method over alternative methods, reflecting the added benefit of integrating elements from GL, GSP and FKT. Significance: The proposed method and results underpin the importance of integrating spatial and temporal characteristics of EEG signals in extracting features that can more powerfully differentiate motor imagery classes.