Context. Neptune’s tropospheric winds are among the most intense in the Solar System, but the dynamical mechanisms that produce them are still unclear. Measuring wind speeds at different pressure levels may help shed light on the atmospheric dynamics of the planet. Aims. The goal of this work is to directly measure winds in Neptune’s stratosphere with ALMA Doppler spectroscopy. Methods. We derived the Doppler lineshift maps of Neptune at the CO(3-2) and HCN(4-3) lines at 345.8 GHz ( λ ∼ 0.87 mm) and 354.5 GHz (0.85 mm), respectively. For that purpose, we used spectra obtained with ALMA in 2016 and recorded with a spatial resolution of ∼0.37″ on Neptune’s 2.24″ disk. After subtracting the planet’s solid rotation, we inferred the contribution of zonal winds to the measured Doppler lineshifts at the CO and HCN lines. We developed an MCMC-based retrieval methodology to constrain the latitudinal distribution of wind speeds. Results. We find that CO(3-2) and HCN(4-3) lines probe the stratosphere of Neptune at pressures of 2 −1.8 +12 mbar and 0.4 −0.3 +0.5 mbar, respectively. The zonal winds at these altitudes are less intense than the tropospheric winds based on cloud tracking from Voyager observations. We find equatorial retrograde (westward) winds of −180 −60 +70 m s −1 for CO, and −190 −70 +90 m s −1 for HCN. Wind intensity decreases towards mid-latitudes and wind speeds at 40°S are −90 −60 +50 m s −1 for CO and −40 −80 +60 m s −1 for HCN. Wind speeds become 0 m s −1 at about 50°S. We find that the circulation reverses to a prograde jet southwards of 60°S. Overall, our direct stratospheric wind measurements match previous estimates from stellar occultation profiles and expectations based on thermal wind equilibrium. Conclusions. These are the first direct Doppler wind measurements performed on the Icy Giants, opening up a new method for the study and monitoring of their stratospheric dynamics.