Abstract Zonal currents in the equatorial Indian Ocean (EIO) are typically considered to exhibit strong semiannual seasonality influenced by the monsoon. However, our study reveals that the Equatorial Undercurrent (EUC) exhibits an unexpected seasonality with prominent annual variability. Constructive (destructive) interference between annual and semiannual components strengthens (weakens) the EUC during early boreal spring (fall). We identify two key mechanisms underlying this behavior: (a) resonant second‐baroclinic‐mode waves enhance equatorial semiannual variability, but their first zero‐crossing near the depth of the EUC limits their contribution to the EUC seasonality; and (b) fourth‐baroclinic‐mode waves profoundly contribute to the annual variability, with equatorial Kelvin and Rossby waves resonating under annual forcing, enhancing the annual response of the EUC. Sensitivity experiments using a linear continuously stratified ocean model indicate that wind forcing in the western EIO (40°−55°E) plays a dominant role in generating the three‐dimensional structure of annual variability of the EUC.

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