Between Kizu and Nara, all Nara Line trains and some Katamachi Line trains run through to the Yamatoji Line; between Kyoto and Nara, the Nara Line operates a through service for its Miyakoji rapid trains, its rapid trains, and its regional rapid trains and the Katamachi Line operates quarter rapid and regional rapid trains; and between Shin-Imamiya and Tennoji (which runs parallel to the Osaka Loop Line), Nanki-bound special express trains, Kanku rapid trains, Kishuji rapid trains, and rapid trains from the Hanwa Line and Osaka Loop Line run directly through to the Yamatoji Line.
上記のほか、木津-奈良間では奈良線の全列車と片町線の一部の列車が乗り入れており、奈良線直通で京都-奈良間に奈良線みやこ路快速・快速列車・区間快速が、片町線方面には快速・区間快速が、また大阪環状線と並行する新今宮-天王寺間には阪和線・大阪環状線から南紀方面特別急行列車や関空快速、紀州路快速、快速などが直通運転されている。