The measurement of ultrasonic surface velocity in concrete and the ultrasonic Time Of Flight method for estimating the depth of surface opening cracks in concrete are important techniques for maintenance of constructions, which are currently performed manually. This paper demonstrates the possibility to automate these measurements by means of an Unmanned Aerial Vehicle (UAV) equipped with a robotic arm, avoiding the risks and costs related to the manual methods. The automated measurements are performed by a special end effector with closed-loop force control that maintains the flying UAV stable while the robotic arm contacts the concrete surface with two piezoelectric transducers for the ultrasonic tests. The system is successfully validated by performing ultrasound measurements from the flying UAV on a test specimen with artificial cracks and on the T9 Metsovo bridge in Greece during an on-field trial, demonstrating an error margin lower than 1 % on crack depth.