One of the crucial branches of activity at the Łukasiewicz Research Network—Institute of Aviation is developing a suborbital rocket vehicle capable of launching small payloads beyond the Earth’s atmosphere, reaching over 100 km in altitude. Ensuring safety is a primary concern, particularly given the finite flight zone and impact area. Crucial to safety analysis is the wind profile, especially in the very first seconds of a flight, when rocket velocity is of the same order as the wind speed. Traditional near-ground wind data sources, ranging from wind towers to numerical models of the atmosphere, have limitations. Wind towers are costly and unfeasible at many test ranges used for launches, while numerical modeling may not reflect the specific ground profile near the launcher due to their large cell size (2 to +10 km). Meteorological balloons are not favorable for such measurements as they aim to provide the launch operator with a wind profile at high altitudes, and are launched only 1–2 times per flight attempt. Our study sought to prototype a wind measurement system designed to acquire near-ground wind profile data. It focuses on measuring wind direction and speed at near-ground altitudes with higher flight frequency, offering data on demand shortly before launch to help ensure safety. This atmosphere sounding system consists of an Unmanned Aerial Vehicle (UAV) equipped with an onboard ultrasonic wind sensor. Some reports in the literature have discussed the possibility of using UAV-borne anemometers, but the topic of measurement errors introduced by placing the anemometer onboard an UAV remains under studied. Limited research in this area underlines the need for experimental validation of design choices–for specific types of UAVs, anemometers, and mounting. This paper presents a literature review, a detailed overview of the prototyped system, and flight test results in both natural (outdoor) and controlled (indoor, no wind) conditions. Data from the UAV system’s anemometer was benchmarked against a stationary reference weather station, in order to examine the influence of the UAV’s rotor on the anemometer readings. Our findings show a wind speed Root Mean Square Error (RMSE) of 5 m/s and a directional RMSE of below 5.3° (both averaged for 1 min). The results were also compared with similar UAV-based wind measurements. The prototyped system was successfully used in a suborbital rocket launch campaign, thus demonstrating the feasibility of integrating UAVs with dedicated sensors for performing regular meteorological measurements in automatic mode.