In this research, the friction-stir welding (FSW) process was used for butt joining of AA2024-T351 and AA6061-T6 dissimilar alloys. Welding was carried out using a tool with frustum of pyramid pin. The effects of rotational and linear speeds of the tool on microstructure, macrostructure, and mechanical properties of joints were examined. The AA2024 alloy was located in the advancing side due to higher flow stress at higher temperature than the AA6061 alloy, which was located in the retreating side. Macro analysis showed that with a rotational to linear speed ratio of higher than 31.25 revolutions per millimeter the transverse joint section demonstrated tunnel hole defect. With an increase in heat input material flow on different depth levels of joint became more homogenous and the AA2024 alloy’s amount in the stir zone increased. Moreover, with rotational to linear speed ratio of higher than 40 revolutions per millimeter, the effect of deformation rate was dominant, whereas with lower ratios the effect of temperature on grain size in the stir zone was dominant. Application of offset to the tool during welding in the retreating side led to improvement of flow of materials in the stir zone and an increase in friction stir joint strength.