Upwelling velocities w in the equatorial band are too small to be directly observed. Here, we apply a recently proposed indirect method, using the observed helium isotope (3He or 4He) disequilibria in the mixed layer. The helium data were sampled from three cruises in the eastern tropical Atlantic in September 2005 and June/July 2006. A one‐dimensional two‐box model was applied, where the helium air‐sea gas exchange is balanced by upwelling from 3He‐rich water below the mixed layer and by vertical mixing. The mixing coefficients Kv were estimated from microstructure measurements, and on two of the cruises, Kv exceeded 1 × 10−4 m2/s, making the vertical mixing term of the same order of magnitude as the gas exchange and the upwelling term. In total, helium disequilibrium was observed on 54 stations. Of the calculated upwelling velocities, 48% were smaller than 1.0 × 10−5 m/s, 19% were between 1.0 and 2.0 × 10−5 m/s, 22% were between 2.0 and 4.0 × 10−5 m/s, and on 11% of upwelling velocities exceeded this limit. The highest upwelling velocities were found in late June 2006. Meridional upwelling distribution indicated an equatorial asymmetry with higher vertical velocities between the equator and 1° to 2° south compared to north of the equator, particularly at 10°W. Associated heat flux into the mixed layer could be as high as 138 W/m2, but this depends strongly on the chosen depths where the upwelled water comes from. By combining upwelling velocities with sea surface temperature and productivity distributions, a mean monthly equatorial upwelling rate of 19 Sv was estimated for June 2006 and a biweekly mean of 24 Sv was estimated for September 2005.