In this study, perforations at rates of 10% and 20% were applied to the inner layers of cross-laminated timber (CLT) panels, manufactured from fir and oak wood, with thicknesses of 51 mm for three-layer panels and 85 mm for five-layer panels, in order to improve their thermal insulation properties. The thermal conductivity and thermal transmittance coefficients of both groups of CLT panels with perforations were determined using both experimental methods and the Finite Element Method (FEM). According to the results obtained from the experiments, the perforation process applied to the inner layers of the CLT panels was found to cause reductions in both the thermal conductivity and thermal transmittance coefficients. The greatest decrease in the thermal conductivity coefficient was observed in the panels with 20% perforation, showing a reduction of 10.8%, while the thermal transmittance coefficient decreased by 8.7% in the same panels. Furthermore, it was observed that the results obtained from the Finite Element Method (FEM) analyses showed similarity to those obtained through experimental methods. In conclusion, the study demonstrated that the use of different wood species and varying perforation rates in the production of CLT panels have a positive and statistically significant effect on the thermal insulation properties of these panels. Therefore, applying various perforation techniques can be recommended to improve the thermal insulation performance of CLT panels.