Friction stir welding (FSW) is the latest technology in the area of metal joining and the most promising of all the welding processes. FSW technology produces welds that are stronger and more durable than other techniques, and it can be done faster, resulting in less cost. This technique has now become an important process in the joining of aluminum alloys and other materials that had been difficult to weld in the past using more traditional fusion techniques. FSW is widely used in a number of industrial applications such as Aeroplane,Space craft, Marine, Shipbuilding, and others. In this research work developed a Finite Element Model (FEM) with improved potential and validate by comparing the simulation results with experimental results obtained by Jamshidi et al. on dissimilar aluminum alloys AA6061-T6 to AA5086-O. Temperature profiles are obtained for two cases, first when AA6061-T6 is located on the advancing side and second when AA6061-T6 is located on the retreating side. Longitudinal and transverse residual stresses are obtained when AA5086-O on the advancing side and AA6061-T6 on the retreating side.