Graphene oxide (GO) has emerged as an ideal filler to reinforce polymeric matrices owing to its large specific surface area, transparency, flexibility, and very high mechanical strength. Nonetheless, functionalization is required to improve its solubility in common solvents and expand its practical uses. In this work, hexamethylene diisocyanate (HDI)-functionalized GO (HDI-GO) has been used as filler of a conductive polymer matrix, poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS). The nanocomposites have been prepared via a simple solution casting method, and have been characterized by scanning electron microscopy (SEM), UV–Vis and Raman spectroscopies, X-ray diffraction (XRD), thermogravimetric analysis (TGA), tensile tests, and four-point probe measurements to get information about how the HDI-GO functionalization degree (FD) and the HDI-GO concentration in the nanocomposite influence the final properties. SEM analysis showed a very homogenous dispersion of the HDI-GO nanosheets with the highest FD within the matrix, and the Raman spectra revealed the existence of very strong HDI-GO-PEDOT:PSS interactions. A gradual improvement in thermal stability was found with increasing HDI-GO concentration, with only a small loss in transparency. A reduction in the sheet resistance of PEDOT:PSS was found at low HDI-GO contents, whilst increasing moderately at the highest loading tested. The nanocomposites showed a good combination of stiffness, strength, ductility, and toughness. The optimum balance of properties was attained for samples incorporating 2 and 5 wt % HDI-GO with the highest FD. These solution-processed nanocomposites show considerably improved performance compared to conventional PEDOT:PSS nanocomposites filled with raw GO, and are highly suitable for applications in various fields, including flexible electronics, thermoelectric devices, and solar energy applications.