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The Fanos granite occurs in the Peonias subzone of the eastern Axios-Vardar zone in northern Greece. The Fanos granite is Late Jurassic (158 ± 1 Ma) and trends N–S, intruding the Mesozoic back-arc Guevgueli ophiolitic complex. The intrusive character of the eastern contact of the Fanos granite with the host ophiolitic complex is well preserved. In turn the western contact is overprinted by a few meters thick, west- to southwest-directed semi-ductile thrust zone, of Late Jurassic-Early Cretaceous age. The Fanos granite is dominated by the typical, isotropic granitoid fabric, although in some places the initial magmatic flow fabric is preserved. The main deformation recognized in the Fanos granite occurred in brittle regime and expressed by Tertiary thrust faults and Neogene-Quaternary normal to oblique normal faults. The origin as well as the possible tectonic setting of the Fanos granite is the main topics that we address in our study. Rock samples of the Fanos granite along with the adjusted Kotza Dere quartz diorite were analyzed for major and trace elements and for Sr and Nd isotopes (only the quartz diorite). The geochemical data show that the granite has peraluminous characteristics, high-K calc-alkaline affinities, and I-type features. The Sr initial isotopic values of the Fanos granite are rather low (0.7053–0.7056) while for the quartz diorite range from 0.7066 to 0.7068. The Nd initial isotopic values range from 0.51235 to 0.51240 for the granite and from 0.51222 to 0.51233 for the quartz diorite. The source of the granitic melt is interpreted to be meta-basaltic amphibolites. These amphibolites are the metamorphic products of enriched mantle melts that underplated the oceanic lithosphere. Taking into account our and published structural and geochemical data for the Fanos granite along with the tectonic data of the broader Axios-Vardar zone, we suggest that the studied granitic rocks were formed during an intra-oceanic subduction within the Neotethyan Axios-Vardar ocean. The granite was obducted during the Late Jurassic, together with the Neotethyan ophiolites westwards, on the Paikon Massif, in the eastern margin of the Pelagonian continent. © 2016, Springer-Verlag Berlin Heidelberg.