Organ transplantation is one of the most complicated and challenging treatments in healthcare systems. Despite the significant medical advancements, many patients die while waiting for organ transplants because of the noticeable differences between organ supply and demand. In the organ transplantation supply chain, organ allocation is the most significant decision during the organ transplantation procedure, and kidney is the most widely transplanted organ. This research presents a novel method for assessing the efficiency and ranking of qualified organ-patient pairs as decision-making units (DMUs) for kidney allocation problem in the existence of COVID-19 pandemic and uncertain medical and logistical data. To achieve this goal, two-stage network data envelopment analysis (DEA) and credibility-based chance constraint programming (CCP) are utilized to develop a novel two-stage fuzzy network data envelopment analysis (TSFNDEA) method. The main benefits of the developed method can be summarized as follows: considering internal structures in kidney allocation system, investigating both medical and logistical aspects of the problem, the capability of expanding to other network structures, and unique efficiency decomposition under uncertainty. Moreover, in order to evaluate the validity and applicability of the proposed approach, a validation algorithm utilizing a real case study and different confidence levels is used. Finally, the numerical results indicate that the developed approach outperforms the existing kidney allocation system.