The Basilica of St. Francis is absolutely incredible and you definitely don't want to miss it. Make sure to visit the tomb of Saint Francis in the crypt below the lower church and the amazing fresco by Giotto in the upper Basilica. Entrance is free
The Eremo delle Carceri is a small sanctuary in the woods outside of Assisi where St. Francis use to retire to pray. It's a very short drive from the city
This is another church you don't want to miss. St Chiara was one of St. Francis' best friends and companions
Spello is a picturesque little town close by, definitely worth a visit!
Perugia is the main town in the area. It is rich in history and monuments.
Spoleto is another beautiful historic town in the area.