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Skopje to Pristina via Urosevac/Ferizaj (# 891/892, Fast), runs daily 16:10-19:20 (NB: train change at the border, while ticket for the train can be bought only on board from conductors)"
Both Macedonian & Kosovo Railways have these trains in the most recent updates, so there shouldn't be any issues (2,50 euro for Kosovo part and about 100 MKD for Macedonian part)