The Voyager spacecraft discovered a large hexagonal feature located at Saturn’s north pole, known as Saturn’s Polar Hexagon. The Cassini spacecraft revisited it in 2005 and returned crisp images of the layering of clouds and small scale vortices embedded within the large feature. 2D and 3D numerical models have demonstrated that barotropic instability can generate a meandering mode of wavenumber 6 alike the hexagon, but the simulated phase velocity is significantly larger than what was observed unless an ad hoc vertical shear of the jet is introduced. Here, we show the first observation of Saturn’s Polar Hexagon at depth using the Very Large Array. The observation was obtained over two observational windows in 2015 and covered a wide range of frequencies, from S to Q bands (2.1–43.7 GHz). The hexagonal feature is visible in the X (10 GHz, 3 cm) and U (14.5 GHz, 2 cm) bands, probing the pressure levels at around 5 bars. Spectral inversions are performed to infer the vertical structure, especially the distribution of the ammonia gas, over the hexagon. We find a depletion of ammonia gas near the edge of the hexagon where the circumferential velocity peaks.