This paper presents the development of a finite element (FE) numerical modelling methodology for the post-buckling and failure analysis of butt-joint stiffened thermoplastic composite panels. The structural components of the investigated panels are bonded with co-consolidated butt-joint methods - a novel joining technique used in aerospace structures. Two panels are examined in this work: the first in pristine condition and the second with a pre-inflicted damage, to evaluate the influence of the damage on the mechanical response of the panel. To assess the ability of these panels to operate safely in the post-buckling region, the nonlinear FE methodology employs large displacement analysis, progressive damage modelling (PDM) and cohesive zone modelling (CZM) approaches. The focuses are placed on the prediction of the displacement fields, the intra-/inter-laminar failure and the debonding between the components of the panel. For validation purposes, the simulation results are compared with the available experimental measurements. The correlation demonstrates the ability of the developed methodology for the modelling and simulation of panels with the same structural configuration.