Control Flow Graphs (CFGs) are critical for analyzing program execution and characterizing malware behavior. With the growing adoption of Graph Neural Networks (GNNs), CFG-based representations have proven highly effective for malware detection. This study proposes a novel framework that dynamically constructs CFGs and embeds node features using a hybrid approach combining rule-based encoding and autoencoder-based embedding. A GNN-based classifier is then constructed to detect malicious behavior from the resulting graph representations. To improve model interpretability, we apply state-of-the-art explainability techniques, including GNNExplainer, PGExplainer, and CaptumExplainer, the latter is utilized three attribution methods: Integrated Gradients, Guided Backpropagation, and Saliency. In addition, we introduce a novel aggregation method, called RankFusion, that integrates the outputs of the top-performing explainers to enhance the explanation quality. We also evaluate explanations using two subgraph extraction strategies, including the proposed Greedy Edge-wise Composition (GEC) method for improved structural coherence. A comprehensive evaluation using accuracy, fidelity, and consistency metrics demonstrates the effectiveness of the proposed framework in terms of accurate identification of malware samples and generating reliable and interpretable explanations.