Friction stir welding is a relatively new solid-state joining technique which is widely adopted in different industry fields to join different metallic alloys that are hard to weld by conventional fusion welding. Friction stir welding is a highly complex process comprising several highly coupled physical phenomena. The complex geometry of some kinds of joints and their three dimensional nature make it difficult to develop an overall system of governing equations for theoretical analyzing the behavior of the friction stir welded joints. The experiments are often time consuming and costly. To overcome these problems, numerical analysis has frequently been used since the 2000s. This paper reviews the latest developments in the numerical analysis of friction stir welding processes, microstructures of friction stir welded joints and the properties of friction stir welded structures. Some important numerical issues such as materials flow modeling, meshing procedure and failure criteria are discussed. Numerical analysis of friction stir welding will allow many different welding processes to be simulated in order to understand the effects of changes in different system parameters before physical testing, which would be time-consuming or prohibitively expensive in practice. The main methods used in numerical analysis of friction stir welding are discussed and illustrated with brief case studies. In addition, several important key problems and issues remain to be addressed about the numerical analysis of friction stir welding and opportunities for further research are identified.