The short answer
For a first trip, Marrakech: its medina is easier to navigate, it has more direct flights, and the Atlas, the Agafay and the road to the Sahara are on its doorstep. Choose Fes if you want living history and long days in the most intact medieval medina in Morocco, and do not mind fewer tourist guardrails. Ideally, do both.
In more detail
Marrakech dazzles; Fes immerses. Marrakech has Jemaa el-Fna, the gardens, the palaces, a wide choice of restaurants and riads, and easy day trips into the mountains. Fes el-Bali is a UNESCO-listed medina of thousands of lanes, Marinid madrasas, the al-Qarawiyyin university and the Chouara tanneries. It asks for a guide, unhurried days and curiosity.
The two cities are about 530 km apart, roughly 6h30 on the motorway without stops. There is no direct train; you change at Casablanca. Flying takes about an hour. Because of that distance, neither works as a day trip from the other.
To see both, spend three or four nights in Marrakech, then fly, take the train or drive north to Fes for three or four nights, adding a day for Meknes and Volubilis. Nine or ten days covers it well. Flying home from Fes saves the journey back.
Good to know
- Fes is often called the culinary capital: try bastilla and harira there.
- Plan a licensed guide for your first day in the Fes medina.
- Riads in Fes can be grand old palace houses.