In order to realize advanced flexible devices, it is critical to simultaneously ensure the flexibility and robustness of bonded joints in the electronic packages for the mechanical and electrical reliability. Flexible bonded joints of thin polymer substrates should be developed because the flexible substrates inevitably undergo extensive mechanical loads, including tension, bending, and twisting. While epoxy resins have been used to bind plastic substrates, they often exhibit inferior flexibility and poor fatigue resistance, which are caused by increased bonding thickness and inherent brittleness, respectively. To solve this problem, we adopted microwave heating of carbon nanotubes (CNTs) for bonding thin polymer substrates for flexible applications. Multiwalled carbon nanotubes are spray-coated onto flexible substrates with a thickness of less than 100 μm. Microwave irradiation was controlled to induce rapid thermal fusion bonding of a pair of thin polymer substrates, where glass plates were attached to prevent thermal distortion. To investigate the bonding mechanism, the polymer-CNT bonding interface was analyzed by using a scanning electron microscope. The mechanical robustness of the bonded joint was evaluated for different microwave power and irradiation times with a fixed frequency of 2.45 GHz. Flexibility of the bonded assembly was characterized by using a three-point bending test and a cross-sectional digital image correlation method with microscopic images. In addition, the bending endurance of a CNT electrode on a flexible substrate assembly was tested under static and dynamic bending. This work provides a concept for realizing flexible interconnections between electronic components, including flexible substrates and electrodes.