The train fares for Kyoto Station from stations in the south of this station differ from those for the subway and Kintetsu lines, and when you exit through a gate at the subway Kyoto station with a ticket for the Kintetsu Kyoto station, you are required to pay an additional fare (on the Kyoto Municipal Subway lines, train fare inconsistency also exists for the through-service operation at Yamashina Station on the Tozai Line of the subway and/or the Keihan Yamashina Station on the Keihan Keishin Line).
当駅以南から京都駅まで向かう場合にも両社の運賃の不整合が生じており、近鉄京都駅までの乗車券で地下鉄京都駅で下車しようとすると追加運賃が生じる（ちなみに京都市営地下鉄においてはこの他、京都市営地下鉄東西線山科駅・京阪京津線京阪山科駅において、直通運転対象との運賃不整合問題がある）。