Bolted joints are potential fatigue critical points in lightweight aircraft structure. This paper presents a comparative study of fatigue behavior and flexibility of double-shear, aluminum-aluminum and aluminum composite joint specimens in variable-amplitude loading. Similar failure mode and fatigue life of both specimen types were obtained by experiments and no indication of pretension loss was observed. A semi-empirical fatigue life prediction model was presented in correlation to the comparisons. Extensometer measurements showed decreasing flexibility, which was explained by increasing load transfer by friction and substantiated by comparative finite element analyses. The flexibility was significantly lower in aluminum-aluminum specimens.