Jupiter’s poles feature clusters of large, long-lasting cyclones that slowly drift westward. We argue that the depth to which these cyclones extend below the cloud layers significantly influences this drift rate. By comparing computer simulations with observations, we estimate the depth of the cyclones and shed light on the stability of Jupiter’s atmosphere at high latitudes. These insights are particularly critical for Juno’s extended mission, which now allows the Microwave Radiometer (MWR) to observe these cyclones with unprecedented resolution, providing a direct test of our framework and facilitating quantitative interpretation of their vertical structure. Our results directly support this new phase of Juno’s mission, offering key constraints to understand the formation, persistence, and dynamics of these giant polar storms.