In this paper, the biodegradation rate and behavior of 3D printed polyester-based nanocomposite scaffolds with Gyroid designs was estimated in the long term, employing numerical simulation and experimental data. Understanding the degradation properties of polymeric scaffolds in biomedical applications is essential as it has a considerable impact on the cell growth and structural integrity of the scaffolds with time. Gyroid structures were studied as they are one of the most commonly used triply periodic minimal surface (TPMS) scaffolds for biomedical application. Hydrolytic degradation was simulated by employing the COMSOL software package. In the first stages, the biodegradation of a polyester was estimated by considering bulk and surface erosion, and mass loss of the scaffolds was predicted using the methods in the literature. Polylactic acid (PLA) was used initially to validate the numerical results. In the last stage, the methods and analyses were linked to PCL matrix properties, and the biodegradation behavior of the additively manufactured Polycaprolactone/Nano-Hydroxyapatite/Chitin-Nano-Whisker nanocomposites was estimated in the long term. Although many factors affect the degradation rate of 3D printed scaffolds, which makes precise prediction not feasible, the method used in this study can help to predict and understand the scaffolds' biodegradation rate in the long term by connecting numerical simulation, analytical assessments, and experimental data.