In this study, a method of fabricating a polymer-based flexible pulsating heat pipe (FPHP) packaged with a metal layer is introduced. In addition, experimental works were conducted to evaluate the thermal performance and long-term reliability of the FPHP. The FPHP consisted of a polycarbonate sheet and a flexible clad copper laminate (FCCL). The width, length and thickness of the FPHP were respectively 53.4 mm, 85.5 mm and 0.64 mm, and HFE-7000 was used as the working fluid. The channels were dual-diameter channels with widths of 1.5 mm and 0.5 mm and a thickness of 0.5 mm. In order to prevent the penetration of non-condensable gases (NGCs) from the outside, the upper and lower sides of the channel wall were encapsulated with the FCCL film using a silane coupling agent, and the flanges of the FPHP were bonded using a tinning and heat-sealing method. The highest effective thermal conductivity of the FPHP was 1028 W/m·K, which is about 2.6 times higher than that of copper in a vertical orientation. The effective thermal conductivities of the FPHP decreased by 6.6% and 35.7%, for a 45 degree bent condition and a horizontal orientation, respectively, compared to those in the vertical orientation. The lifetime of the FPHP was evaluated in terms of long-term reliability. The thermal performance of the FPHP was measured for 40 days in an atmospheric-pressure environment, and it was confirmed that the thermal performance of the FPHP was well maintained during that period. The method proposed in this study enables the fabrication of a thin and flexible pulsating heat pipe with high thermal performance and long-term reliability.