The Great Whirl (GW) is a quasi‐permanent anticyclonic eddy that appears every summer monsoon offshore of the Somalia upwelling. The annual cycle of the GW is well described, but deviations from its mean seasonal cycle (hereafter non‐seasonal variability) have been less explored. Satellite observations reveal that the leading mode of summer non‐seasonal sea‐level variability in this region is associated with ∼100‐ km northward or southward GW shifts from its climatological position. Northward shifts are associated with a stronger GW, and two cold, productive coastal upwelling wedges at 5°N and 10°N. Southward shifts are associated with a weaker GW, no wedge at 5°N and a single stronger‐than‐usual cold and productive wedge at 10°N. An eddy‐permitting (25‐km resolution) 50‐member ensemble ocean simulation reproduces this GW variability well. It indicates that the non‐seasonal GW variability has a short ∼20 days timescale intrinsic component, associated with the GW interaction with mesoscale eddies, and a lower‐frequency, ∼100 days externally forced component. Intrinsic variability dominates at both subseasonal (two thirds of the variance) and interannual timescales (57% of the variance). The externally forced signal results from shifts in the probability distribution of the subseasonal GW position (e.g., more likely northward than southward shifted instantaneous GW positions over a season). The mechanism for this external forcing is not entirely clear, but it appears to be related to the Rossby wave response to offshore wind stress curl forcing, which evolves into a north‐south dipole that projects onto the GW variability pattern.