Figures Abstract Quantum computing leverages quantum mechanics to perform complex computations efficiently, yet its practical implementation is hindered by hardware-software interdependence and quantum state instability. This paper advances lightweight FPGA-based quantum emulation by incorporating a universal quantum gate set, including parameterized Phase gates and the CNOT gate, to support comprehensive quantum protocol emulation on FPGA hardware. The FPGA platform used for synthesis is Artix-7. The proposed emulator is validated through simulations of quantum circuits, including Bell States, the Deutsch algorithm, Superdense coding, Grover’s search, and BB84 QKD, with results benchmarked against IBM’s noiseless quantum simulator. Utilizing FPGA’s customizable parallelism and energy efficiency, this framework offers a resource-efficient, reliable platform for developing and testing quantum algorithms. Citation: Zahra A, Khalid M, Riaz N, Waheed S, Mujahid U, Najam-ul-Islam M (2026) FPGA-based emulation framework for two-qubit quantum computation: Design, implementation, and validation. PLoS One 21(8): e0356172. https://doi.org/10.1371/journal.pone.0356172 Editor: Zeheng Wang, Commonwealth Scientific and Industrial Research Organisation, AUSTRALIA Received: November 28, 2025; Accepted: July 30, 2026; Published: August 24, 2026 Copyright: © 2026 Zahra et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability: The Source codes are available at via https://github.com/Arfeen983/FPGA-Based-Emulation-Framework-for-Two-Qubit-Quantum-Computation and https://www.protocols.io/view/fpga-based-emulation-framework-for-two-qubit-quant-dm6gp4bqpgzp/v2. Funding: The author(s) received no specific funding for this work. Competing interests: The authors have declared that no competing interests exist. 1 Introduction In 1980, Richard Feynman and Paul Benioff presented the idea of a Quantum Computer, i.e., a hardware system based on the principles of quantum mechanics. Unlike classical computers, which operate on binary logic, this technology leverages the laws of quantum physics, allowing the system to perform powerful operations and execute certain computations efficiently. In the present information era,