Gabès is on the main coastal road and rail line between Tunis and Tunisia's south. Trains run several times a day to Tunis (around 6 hours), Sfax, and Sousse; the line currently ends at Gabès, so anything further south is by road. The station is in the centre of town.
Louages (shared taxis) are the fastest way south to Medenine and Tataouine, west to Douz via Kebili, and on to the Sahara. The louage and bus stations sit on opposite sides of the city — ask before heading out. From Gabès airport just south of town there are occasional flights to Tunis, but the train and road connections are usually a better bet.