The objective of this work is to analyse the formation and growth of various phases including intermetallics during FSW of SS304 and pure titanium. For dissimilar friction stir welding, the intermetallics and their thicknesses play a critical role towards the joint strength and failure. A numerical model is developed to capture the formation and thicknesses of intermetallics. The numerical model consists of a coupled thermomechanical model, Fick’s second law of diffusion and Gibbs free energy of the phases. To verify the numerical model, friction stir welding of SS304 and pure titanium is performed with combinations of two tool rotation speeds (600 rpm and 700 rpm) and 50 mm/min feed rate. The difference in the diffusion rates of various elements leads to movement of Fe-rich region towards the pure titanium side. As temperature rise during the process, the $$\upbeta$$ -Ti thickness increases as $$\mathrm{\alpha }$$ -Ti transforms into $$\upbeta$$ -Ti. Further as the peak temperature is reached, FeTi forms in the region with significant presence of Fe and Ti. During cooling, the $$\upbeta$$ -Ti reduces due to formation of FeTi at the interface and transformation of $$\upbeta$$ -Ti to $$\mathrm{\alpha }$$ -Ti in the regions away from the interface. The $$\upbeta$$ -Ti remains stable at room temperature in the regions with sufficient presence of Fe, Cr and Ni in pure titanium. This study shows that the formation of FeTi, $$\upbeta$$ -Ti and $$\mathrm{\alpha }$$ -Ti needles in the vicinity of the interface and their thicknesses depend on the location in the stir region and tool rotation speed. The experimental results are well captured by the numerical model.