Foggia is the hub. Trains from Rome, Bologna, Naples and Bari all stop there, and the bus bay for San Giovanni Rotondo is outside the station; the published line 732 timetable lists departures roughly hourly through the day, more often in the early morning. Buy the ticket at the SITA office or on board where allowed, and check the current timetable on sitabus.it because the posted schedule carries old dates.
A day trip from Bari works: the 6:15 a.m. bus gives six hours at the shrine before the 2:30 p.m. return, enough for the tomb, the old church and cell, and the 10:00 or 11:30 a.m. Mass. A day trip from Rome is a long day, roughly 3 hours by train plus the bus each way, with the last practical return train in the evening; most pilgrims stay one night in San Giovanni Rotondo, which also allows the 7:30 a.m. Mass at the urn before the buses arrive.
From Bari airport, take the airport train to Bari Centrale and walk to the Via Capruzzi bus stop behind the station; the direct bus does not stop at the airport. Groups usually hire a coach from Bari or Foggia. Pietrelcina, Padre Pio's birthplace near Benevento, is a separate trip; see is-pietrelcina-the-same-place-as-san-giovanni-rotondo. Basic directions are also on how-do-i-get-to-san-giovanni-rotondo.