The purpose of this study was to investigate the feasibility and effectiveness of COVID-19 throat swab samples delivered by medical drones in epidemic prevention and control. This study was carried out in both southern and northern hospital districts of the Affiliated Hospital of Jiangnan University from May to October 2022. The main participants were the Affiliated Hospital of Jiangnan University and Zhejiang Antwork Technology Co., Ltd. We first constructed an urban medical unmanned aerial vehicle (UAV) delivery system and developed a UAV-specific storage box for COVID-19 samples. The UAV system was used to transport COVID-19 throat swab samples from the northern hospital district to the southern hospital district, and the following indexes were obtained: (1) flight time of COVID-19 samples delivered by UAV, (2) real-time temperature of COVID-19 nucleic acid samples during transportation, and (3) the time of distribution of COVID-19 nucleic acid samples by road traffic as measured using the Baidu Maps application, compared with the flight time of UAV. The COVID-19 sample delivery system for urban medical UAV mainly consists of intelligent logistics UAV, low-temperature COVID-19 throat swab sample storage box, unmanned logistics hub, and cloud operation control platform. The flight distance between the northern and southern districts of the Affiliated Hospital of Jiangnan University was 10 km, and the ground distance was 24 km. From May 11 to October 28, 2022, a total of 1,190 UAV flights occurred. The average flight time was 13 minutes, which was 40 to 70 minutes faster than the average road travel time required for manual delivery of COVID-19 throat swab samples. At different time points in the day, UAV delivery efficiency increased by 67.5% to 82%. The use of 5G with the Internet of Things and UAV technology to deliver nucleic acid samples has the characteristics of fast speed, being unaffected by ground traffic conditions, and the ability to ensure the safety of nucleic acid samples in the transportation process, which is worthy of further study.