The unique micro porous structure of expanded polytetrafluoroethylene (ePTFE) that allows bio-integration for fixation, as well as overall mechanical integrity make it used successfully in a number of biomedical and clinical applications, which include the reconstruction of the pulmonary valve in in right ventricular outflow tract reconstruction (RVOT) operations. The objective of this study was to determine the effects of the thermal treatment on physical and mechanical properties of ePTFE membranes. ePTFE sheets were cut into 16 rectangle strips (10 mm by 60 mm) and evenly separated into 4 groups. One group was the blank control (group A), while the rest of the three groups (group B to D) were heated to 350°C and cooled to 24°C at different cooling rates (10°C/min, 20°C/min and rapid ambient air cooling) in a temperature controlled atmosphere. The mechanical and morphological characteristics of all the samples were tested using a tensile test machine and a scanning electron microscopy (SEM). The results show that the elastic modulus of group B to D was 24.95%, 33.45% and 72.76% higher than group A. The percentage elongation of groups B to D was found to be between 2.3% and 40.45% lower than group A. The proportion of pores in the ePTFE membrane was reduced following the thermal treatment. There were no morphology differences observed between groups B to D. In summary, the selection of cooling rate was important for preserving the mechanical properties of ePTFE membranes under thermal treatment. These findings may provide useful information for the preparation of molded ePTFE valve in RVOT operations.