The aluminium alloys 5052 and 6082 are extensively used in manufacturing lighter structural members, having improved strength and resistance to corrosion. Magnesium (Mg) and Chromium (Cr) powder were the filler materials selected for enhanced corrosion protection properties in this investigation. Friction stir welding (FSW) process parameters viz., spindle speed, welding speed, shoulder penetration, the centre distance between the holes and filler ratio are used to forecast the minimum corrosion rate from different weld regions of AA5052-AA6082 dissimilar joints. Response surface methodology based on a central composite design was used to evolve the mathematical models and estimate dissimilar FSW joints’ corrosion rates. Response optimization shows that the minimum corrosion rate was achieved by the welding parameters of spindle speed 1000 rev/min, welding speed 125 mm/min, holes spacing of 2 mm and filler ratio 95% of Mg and 5% of Cr.