Aluminium alloys present some criticalities in terms of fatigue life characterisation due to the absence of a point representing the ‘fatigue limit’, the topic becomes complicated when the material is welded. In this case, the fatigue characterisation lies on design specifications which have to clearly explain the guidelines for the performing the tests and for evaluating the failures, in order to design tailored welded joints. However, the fatigue of welded joints is a difficult subject since the welding process makes the material different, introducing residual tensions, defect, etc. Also, the standard test methods provide only the estimation of the strength at fixed loading cycles but no information on the damage processes occurring in the material. Prompted by these issues researchers deal with the study of other approaches to achieve not only information on fatigue resistance but also damage information. In particular, the thermography can be used for thermal signal analysis of dissipative heat sources involved in fatigue of material undergoing cyclic test. In this paper, this approach is adopted to study the fatigue behavior of friction stir welded joints of AA5754-H111 during specific loading conditions. The component of the temperature related to intrinsic dissipations is assessed and the fatigue strength is evaluated together with a graphical study of the location of damaged areas.