Ducted fan Unmanned Aerial Vehicles (UAV) face unique control challenges, leading to varied parameters between simulations and real-world testing. Hardware-in-the-Loop Simulation (HILS) bridges this gap by validating control algorithms in real-time. This study integrates Pixhawk 1 as the flight controller, managing UAV dynamics with designed algorithms. Host computers run Autopilot Controller and Plant Simulation apps alongside Pixhawk, linking via MAVLink to a Ground Control Station (GCS). Simulations demonstrate quicker responses and lower errors than HILS, affected by sensor noise and synchronization delays. Differences in Integral of Time-Weighted Absolute Error, ITAE (45.69%) and amplitude (50.87%) highlight HILS’s longer settling and rise times (averaging 17.1% and 36.99% more than simulation), emphasizing its role in refining UAV control for robust practical performance.