The main purpose of this research was to fabricate carbon nanofiber (CNF) mats with a high thermal conductivity, by electrospinning of poly(acrylonitrile) (PAN) and subsequent thermal treatment. To improve the thermal conductivity of the CNF mats, isotropic and mesophase pitches were co-axially electrospun with a PAN shell. The mesophase pitch in this research was prepared by thermal treatment from isotropic pitch, and the structural properties were evaluated by Raman spectroscopy and X-ray diffraction analysis. The contact resistance between CNFs in mats was effectively reduced by wetting of the PAN shell using ethanol and the formation of a networked structure during thermal processing. The thermal conductivity of the resulting CNF mats was measured by a laser flash method, and a significantly improved thermal conductivity was obtained for isotropic pitch-PAN CNF mats. This is attributed to a networked structure, a well-developed carbon structure, and a reduced contact resistance.