Jupiter’s Great Red Spot (GRS) is the largest atmospheric vortex in the Solar System and has been observed for at least two centuries. It has been unclear how deep the vortex extends beneath its visible cloud tops. We examined the gravity signature of the GRS using data from 12 encounters of the Juno spacecraft with the planet, including two direct overflights of the vortex. Localized density anomalies due to the presence of the GRS caused a shift in the spacecraft line-of-sight velocity. Using two different approaches to infer the GRS depth, which yielded consistent results, we conclude that the GRS is contained within the upper 500 kilometers of Jupiter’s atmosphere.