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The energy dissipation capacity resulting from progressive cracking of the web-flange junctions (WFJs) of a pultruded GFRP deck system was experimentally investigated. Web-cantilever bending experiments up to failure were performed on two WFJ types (IfO, IcO) with similar geometry and fiber architecture but different initial imperfections. The latter resulted in different load-displacement behaviors (linear and markedly nonlinear up to failure in IfO and IcO, respectively) and failure modes. Failure was governed in both types by through-thickness tension in the tensioned fillet. However, different crack sequences were observed due to the fiber architecture and resulted in an abrupt failure in IfO and a more progressive failure in IcO, in addition to a higher load-bearing capacity of the latter. The total and dissipated energies of the IcO WFJs and their ductility index, defined as the ratio of the dissipated to total energy, were modeled. The ductility index did not significantly increase as from a given displacement. The main energy dissipation mechanism of the IcO WFJs was related to crack development; dissipation through viscoelastic losses was significant only at low deflection levels.