The α+β dual phase TC4 titanium alloy hydrogenated with 0.1 wt%, 0.3 wt% and 0.5 wt% hydrogen was friction stir welded using a W-Re pin tool. Hydrogen was removed from the as-welded joints through post-weld vacuum annealing. Effects of hydrogen as a temporary alloying element on microstructure and mechanical properties of TC4 titanium alloy friction stir welded joints were investigated. Results show that hydrogen content has a significant influence on microstructure and mechanical properties in hydrogenated titanium alloy as-weld joints. Hydrogen almost does not escape from the hydrogenated titanium alloy during the friction stir welding and can be removed through post-weld vacuum annealing. The hydrogen-induced metastable phases and hydrogen-rich phases in as-welded joints decompose and transform during the dehydrogenation process. Mechanical properties of as-welded joints are also significantly recovered after dehydrogenation and the mechanical properties of dehydrogenated joints basically reach the level of the as-received unhydrogenated titanium alloy joints.