San Miguel is 140 km east of San Salvador on the Carretera Panamericana (CA-1). By bus, the journey takes around two to two-and-a-half hours on frequent direct services from the Terminal de Oriente in San Salvador. Buses run throughout the day; the last service back to the capital typically departs mid-evening.
From the Honduran border at El Amatillo, San Miguel is about 60 km west — roughly an hour by bus. Regular services connect the crossing to the city throughout the day. San Miguel's main bus terminal is on the western edge of the city centre.
La Unión, the port on the Gulf of Fonseca and the departure point for the gulf islands, is 45 km east — about 45 minutes by bus. San Miguel acts as the transit hub for the entire eastern region, so connections to smaller towns and the Pacific coast are easy to find at the terminal.
El Papalón Airport (MSSM) is located a few kilometres east of the city but operates no scheduled passenger services at present. All flights to eastern El Salvador use San Salvador's Monseñor Óscar Arnulfo Romero International Airport.