The wide adoption of thermoplastic composites to reduce weight in structural parts requires reliable numerical methods to account for debonding between overmolded parts. Cohesive elements are a good approach for the modeling of debonding problems. However, very small element sizes are required in the narrow cohesive zone, hindering its applicability in practical scenarios. In the present work, a novel structural cohesive element is proposed for the efficient modeling of debonding in thermoplastic composite panels with overmolded stiffeners. Triangular Kirchhoff–Love shell elements are employed for the modelling of thin panels (or panel plies in laminate panels) and the stiffeners. The cohesive element is conforming to the orthogonal T-jointed shell elements. The plate kinematics and the displacement dependent rotational fields are employed to define the displacement jumps over the cohesive surface in terms of the jumps along its central line. Therefore, the jumps can be defined from the shell fields evaluated at the elements edges, while still allowing for cohesive couple transmission. The Turon cohesive law is adopted to relate the jumps to the cohesive tractions. The model is verified for mode I, II and mixed-mode classical benchmark problems. A debonding problem is analyzed with both standard 3D cohesive elements and the proposed element. The results show that the element size in the proposed models can be much larger than that in the standard cohesive element models, with more than 90% reduction in CPU time, while retaining prediction accuracy. The debonding analysis of a complex stiffened panel is also presented for illustrative purposes.