Falling between seasonal cycle variability and the impact of local drivers, the sea level in the Red Sea and Gulf of Aden has been given less consideration, especially with large-scale modes. With multiple decades of satellite altimetry observations combined with good spatial resolution, the time has come for diagnosis of the impact of large-scale modes on the sea level in those important semi-enclosed basins. While the annual cycle of sea level appeared as a dominant cycle using spectral analysis, the semi-annual one was also found, although much weaker. The first empirical orthogonal function mode explained, on average, about 65 of the total variance throughout the seasons, while their principal components clearly captured the strong La Niña event (1999–2001) in all seasons. The sea level showed a strong positive relation with positive phase El Niño Southern Oscillation in all seasons and a strong negative relation with East Atlantic/West Russia during winter and spring over the study period (1993–2017). We show that the unusually stronger easterly winds that are displaced north of the equator generate an upwelling area near the Sumatra coast and they drive both warm surface and deep-water masses toward the West Indian Ocean and Arabian Sea, rising sea level over the Red Sea and Gulf of Aden. This process could explain the increase of sea level in the basin during the positive phase of El Niño Southern Oscillation events.