Resection of completely endophytic renal tumors is a huge challenge for surgeons due to a lack of definite visual clues, especially in the laparoscopic approach. Three-dimensional (3D) kidney models, which can illustrate the clear relationship between renal masses and surrounding health tissues, were considered as reliable tools for understanding renal tumor characteristics in previous studies. We hypothesized that 3D kidney models can be used not only for planning but also for navigating laparoscopic partial nephrectomy (LPN) in patients with completely endophytic renal tumors. In this study, we successfully constructed five cases of 3D kidney models for assisted planning and navigation for LPN in endophytic renal tumors. The renal masses and surrounding normal parenchyma of the patient-specific 3D models were dyed by different colorants for clear illustration. All patients experienced acceptable perioperative outcomes, and no patient suffered serious relative complications. The 3D kidney models were considered as a reliable tool based on clinical outcome and postoperative questionnaire results. This study is the first report of 3D kidney models for patients with completely endophytic tumors. 3D kidney models can aid surgeons in understanding the characteristics of renal tumors and potentially support assisted planning and performance of LPN in endophytic tumor cases.