Trains used to be operated every ten minutes (six trains per hour) during the day at the beginning of the inauguration throughout the line, except for trains coming from the Keishin Line which runs at a 15-minute interval; however, since March 2000 trains have been operated every 7.5 minutes (eight trains per hour) in order to synchronize the time schedule with trains operated on the Karasuma Line of Kyoto Municipal Subway, which are connected to trains operated on the Tozai Line at Karasuma Oike Station, resulting in a ratio of 2:1 per quarter hour for trains operated on the Tozai Line relative to those operated directly to the Keishin Line.
日中のダイヤは15分間隔で運転される京津線からの直通列車を除けば、開業当初は全線で10分間隔（1時間あたり6本）だったが、2000年3月に烏丸御池駅で連絡する京都市営地下鉄烏丸線と運転間隔を揃えるためもあり7分半間隔（1時間あたり8本）に増発され、これにより15分あたり東西線内列車2本：京津線直通列車1本のパターンになった。