Pint-sized Tokushima Airport to the north of the city, has daily services to Tokyo, Nagoya, Fukuoka and Sapporo. Buses to JR Tokushima Station take 25 minutes and cost ¥430. The schedules are synchronized to flight departures/arrivals.
Buses run to the station from Kobe Airport every 1-2 hours at 55 minutes past (2 1/2 hours, ¥3200). Airport Limousine buses operate from the nearest international gateway, Kansai International Airport in Osaka (2 3/4 hours, ¥4000 — cheaper if you purchase a round trip ticket).
From Okayama, take a Marine Liner rapid train to Takamatsu, then transfer to the Uzushio limited express for the run to Tokushima (2 hours, ¥4420). Two daily Uzushio trains run directly from Okayama, with no change of trains required (¥5050). If you are coming from Kansai or the east (i.e. Nagoya or Tokyo) then changing to a bus at Shin-Kobe will result in an easier trip to Tokushima - a wise investment for Japan Rail Pass holders, even if the pass doesn't cover the bus. (See By Bus below)
The JR Tokushima Line runs toward Ikeda (2 hours), for connections south towards the Iya Valley.
If arriving from Kansai via Awaji Island, you're pretty much guaranteed to end up in Tokushima. JR Bus operates many services to Tokushima: Awa Express bus service leaves from Kobe and Kobe Airport (2 hours from Shin-Kobe station, ¥3200, 15 daily round-trips), Osaka (2 3/4 hours, ¥3600, 23 daily round-trips), Kyoto (3 hours, ¥4100, 7 daily round-trips), and on weekends and holidays, Nara (4 hours, ¥3900, 2 round-trips). Keihan Railways has its own highway bus that travels to and from Kyoto and Hirakata.
The overnight Dream Tokushima bus runs from Tokyo and Shinjuku (10 hours, ¥10000 each way).
Ocean East (tel. 03-5148-0109) operates a ferry service between Tokyo, Tokushima and Kitakyushu. Both the Tokyo and Kitakyushu runs are overnight;