The Yavin Runner II functioned as one of several shuttles providing service to the Jedi Praxeum located on Yavin 4.
During 14 ABY, the Yavin Runner II, while transporting a collection of fresh pupils from Coruscant to the Praxeum, was downed by Tavion Axmis as a deceptive maneuver. The shuttle crash-landed a few kilometers to the west of a Massassi Temple. Though the students came out unscathed, a shuttle was required to retrieve them. Simultaneously, Alora, a member of Tavion's cult, infiltrated the Academy and accessed Luke's data.
Later, a shuttle analogous to the Yavin Runner II was piloted by Jaden Korr during a mission to rescue someone on Blenjeel. Although the vessel was wrecked in an electrical storm, Korr managed to fix it using components salvaged from the ship he had journeyed to save.