The Bou Inania de Fes Medersa is located in the old city. That is, in the medina. Specifically, in Talaa Kebira Street, just 2 minutes walk from one of the gates to the medina: the Bab Boujloud or Blue Gate of Fez.
The price to visit the Medersa Bou Inania is 20 dirham. (2$)