Familial focal epilepsy with variable foci (FFEVF) is an autosomal dominant disorder characterized by focal seizures arising from different brain lobes in different family members. Currently, the diagnosis of this syndrome mainly depends on the combination of semiology and EEG after exclusion of other types of familial focal epilepsy. Mutations in dishevelled, Egl-10, and pleckstrin domain-containing protein 5 (DEPDC5) have been recently identified as a common cause of this syndrome. We studied a Chinese four-generation FFEVF family with nine affected individuals. Targeted next-generation sequencing was performed for the proband and the suspected mutation was confirmed by Sanger sequencing. Magnetoencephalography (MEG) was applied to two MRI-negative patients with refractory epilepsy. We identified a novel splice site mutation in DEPDC5 (c.280-1 G>A) in this family. The MEG results showed different dipole-clustered areas in these two patients. This is the first report of the use of MEG to confirm a diagnosis of FFEVF, in a Chinese family with a novel DEPDC5 mutation. Furthermore, the MEG results also revealed the possibility of surgical resection for these two intractable patients.