Dune migration response to regional inter-annual climate variability in Ceará, Northeastern Brazil was investigated. Dunes along the study area are mainly barchans and sand-sheets and they migrate at an averaged rate of 17 m/yr although this value depends on dune dimensions, the larger the dune the lower the migration. This is explained by the existence of a representative regional aeolian transport rate that is almost constant along the region inducing different dune response depending on dune size, which is a common feature of barchans fields. Estimated yearly transport rates from dune migration were compared to the values obtained by using the calibrated aeolian transport formula when fed by regional wind climate data. The results obtained differ by about 20% (100 m³/m/yr) from actual aeolian transport measurements (80 m³/m/yr) from dune evolution, which can be considered as a good agreement between both approaches. We show a relationship between dune displacement and strength of the dry season in the region. With larger displacements occurring in drier years, coincident with a more northern position of the Intertropical Convergence Zone (ITCZ), which occurred during strong El Niño periods. This relationship serves to link the dune migration in Northeastern Brazil with El Niño events. As El Niño Southern Oscillation (ENSO) supposes a major climatic perturbation, its effects will be transferred to all the dynamical processes controlled in a direct or indirect manner by the regional climate. These findings should be incorporated into Integrated Coastal Zone Management (ICZM) strategies for the region.