The electrically conductive polymers reinforced with carbon nanotubes (CNTs) have been in the focus of academic and industrial researchers in the recent years. The electrical conductivity of the polymers can be significantly improved by the addition of carbon nanotubes (CNTs) where CNTs create a continuous network for electrical conductivity in the polymer matrix while keeping the other advantages of polymer materials intact. CNT filled polymer materials have found significant applications in areas such as EMI/RFI shielding, antistatic coatings, light corrosion-resistant components, energy storage device, electronic equipment, pressure sensors, weight sensors, gas sensors and in many more engineering applications. Nevertheless, there is a concern about lower electrical conductivity of the CNT filled polymers especially when it is compared with metals. Limited work has been done on the effects of thermal annealing on the electrical conductivity of the CTN filled polymers. The current paper investigates the effect of annealing on the electrical conductivity of Multi-Wall Carbon Nanotubes filled PEEK (Polyether Ether Ketone) which is one of the most unique and high performance polymer materials developed for high temperature applications with a glass transition temperature of 143°C and a melting temperature of 343°C. The injection moulded parts made with CNT-PEEK composite are exposed to annealing at three different temperatures (120, 220 and 320oC) for 5 hours. The electrical conductivity of the annealed parts are measured and compared with the electrical conductivity of the non-annealed parts. To understand the topographical, morphological and structural changes induced by the annealing process, a series of investigations like the roughness measurement, water contact angle measurement, scanning electron microscopy etc. were carried out. The results from these investigations are presented in the paper together with the analysis and discussion of the findings.