Selected Basis Diagonalization (SBD) plays a central role in Sample-based Quantum Diagonalization (SQD), where iterative diagonalization of the Hamiltonian in selected configuration subspaces forms the dominant classical workload. We present a GPU-accelerated implementation of SBD using the Thrust library. By restructuring key components -- including configuration processing, excitation generation, and matrix-vector operations -- around fine-grained data-parallel primitives and flattened GPU-friendly data layouts, the proposed approach efficiently exploits modern GPU architectures. In our experiments, the Thrust-based SBD achieves up to $\sim$40$\times$ speedup over CPU execution and substantially reduces the total runtime of SQD iterations. These results demonstrate that GPU-native parallel primitives provide a simple, portable, and high-performance foundation for accelerating SQD-based quantum-classical workflows.