As feature density increases within microelectronics, so does the dissipated power density, which puts an increased demand on thermal management. Thermal interface materials (TIMs) are used at the interface between contacting surfaces to reduce the thermal resistance, and is a critical component within many electronics systems. Arrays of carbon nanotubes (CNTs) have gained significant interest for application as TIMs, due to the high thermal conductivity, no internal thermal contact resistances and an excellent conformability. While studies show excellent thermal performance, there has to date been no investigation into the reliability of CNT array TIMs. In this study, CNT array TIMs bonded with polymer to close a Si-Cu interface were subjected to thermal cycling. Thermal interface resistance measurements showed a large degradation of the thermal performance of the interface within the first 100 cycles. More detailed thermal investigation of the interface components showed that the connection between CNTs and catalyst substrate degrades during thermal cycling even in the absence of thermal expansion mismatch, and the nature of this degradation was further analyzed using X-ray photoelectron spectroscopy. This study indicates that the reliability will be an important consideration for further development and commercialization of CNT array TIMs.