Magdalena de Kino sits on Federal Highway 15, the main road between Nogales on the Arizona border and Hermosillo — 80 km south of Nogales and 200 km north of Hermosillo. The toll motorway (Highway 15D) bypasses the town slightly; take the free road to enter the centre.
Long-distance buses (Tufesa, TAP, Estrella Blanca) stop in Magdalena en route between the border and Hermosillo. By car the town is a natural lunch and refuel stop on a road trip south. The nearest commercial airports are Hermosillo (200 km south) and Tucson, Arizona (140 km north across the border).