The station name "Miyamaki" originates from its location, and "JR" is attached to distinguish it from Miyamaki Station on the Kintetsu Kyoto Line, which is located on the opposite side of JR-Miyamaki Station.
所在地に由来するが、当駅向かいにある近鉄京都線の三山木駅と区別するため、JRを冠した。