Buildings, bridges, and dams are examples of civil infrastructure that play an important role in public life. These structures are prone to structural variations over time as a result of external forces that might disrupt the operation of the structures, cause structural integrity issues, and raise safety concerns for the occupants. Therefore, monitoring the state of a structure, also known as structural health monitoring (SHM), is essential. Owing to the emergence of the fourth industrial revolution, next-generation sensors, such as wireless sensors, UAVs, and video cameras, have recently been utilized to improve the quality and efficiency of building forensics. This study presents a method that uses a target-based system to estimate the dynamic displacement and its corresponding dynamic properties of structures using UAV-based video. A laboratory experiment was performed to verify the tracking technique using a shaking table to excite an SDOF specimen and comparing the results between a laser distance sensor, accelerometer, and fixed camera. Then a field test was conducted to validate the proposed framework. One target marker is placed on the specimen, and another marker is attached to the ground, which serves as a stationary reference to account for the undesired UAV movement. The results from the UAV and stationary camera displayed a root mean square (RMS) error of 2.02% for the displacement, and after post-processing the displacement data using an OMA method, the identified natural frequency and damping ratio showed significant accuracy and similarities. The findings illustrate the capabilities and reliabilities of the methodology using UAV to evaluate the dynamic properties of structures.