Stratospheric balloon missions have emerged as a cost-effective alternative to space missions for scientific research and technology development. These missions enable the collection of critical data from the Earth’s upper atmosphere while reducing financial and logistical burdens associated with traditional space missions. One key challenge in these missions is the accurate measurement of the relative-to-the-gondola wind speed in the tropopause and the stratosphere. This paper explores the viability of using cup anemometers as wind speed sensors in stratospheric balloon missions, offering an easy-to-calibrate, low-cost, and accurate solution. The present paper provides a short overview of stratospheric balloon missions and their relevance in atmospheric research and outlines the challenges and limitations of existing wind speed sensing technologies. The cup anemometer is also described, detailing its working principle, advantages, and limitations, and propose a methodology for incorporating the instrument into stratospheric balloon missions. To validate the proposed methodology, a stratospheric balloon mission (the Tasec-Lab experiment, onboard a B2Space balloon launched in 2021), was equipped with a cup anemometer whose performance was analyzed. The results prove that cup anemometers can provide accurate and reliable relative wind speed measurements in the tropopause and the stratosphere. Furthermore, the low power consumption and the ease of development and calibration of cup anemometers make them an attractive option for stratospheric balloon missions.