Magione itself is compact and easy to cover on foot — the castle, the churches, and the main piazza are within a few minutes' walk of each other.
For the wider area, a car is the most practical option. The road along the eastern shore of Lake Trasimeno to San Feliciano is short (about 7 km) and scenic. Montecolognola is a 10-minute drive south-east. Parking in Magione is free and easy to find outside the small historic centre.
By bicycle is one of the better ways to explore the lake shore. A cycle path connects several points along the eastern and southern shores. Bikes can be hired locally — ask at the tourist office or in San Feliciano. The full circuit of the lake is about 60 km and can be done in a day; for a shorter ride, the section between San Feliciano and Castiglione del Lago on the southern shore is the most complete and scenic.
Boats run from San Feliciano to Isola Maggiore (15 minutes) several times a day in the warmer months. The service is reduced in winter. Check current timetables locally, as they change seasonally.
Local buses connect Magione to Perugia and to other towns on the lake, but the service is infrequent and primarily useful for commuters rather than visitors.