The city is linked by air with the rest of the country by the Dipolog City Airport  which is situated only 12 kilometers away from the city’s urban core.

Dapitan City hosts the Province of Zamboanga del Norte’s sole commercial seaport, the Pulauan Wharf, found in the coastal zone of Barangay San Vicente approximately nine (9) kilometers away from the poblacion. This wharf serves not only passengers and traders from Dapitan but also those from Dipolog as well as from other municipalities of Zamboanga del Norte and the neighboring Provinces of Zamboanga del Sur and Misamis Occidental. Another port situated in Barangay Taguilon is used only by inter-island vessels seeking refuge during inclement weather and may serve as an alternate docking for leisure cruising.

Noticeably, passengers embarking / disembarking at Pulauan wharf have been increasing over the years. Data show that incoming cargoes generally consisted of cement, fertilizer, sugar, bottled cargoes, wheatflour and rice while outgoing cargoes included charcoal, copra, fruits and vegetables, corn and live animals.

Rural Transit Bus Company provides air-conditioned and regular buses within the province and inter-provincial routes including the route going to Manila via Dumaguete, Bacolod, Iloilo, Kalibo, Caticlan, Calapan (Mindoro) and Batangas.

Evergood Transit also provides daily transport within the 15 kilometer route from Dapitan to Dipolog (vice-versa).