Studies comparing bipolar disorder (BD) and major depressive disorder (MDD) are scarce, and the neuropathology of these disorders is poorly understood. This study investigated source-level cortical functional networks using resting-state electroencephalography (EEG) in patients with BD and MDD. EEG was recorded in 35 patients with BD, 39 patients with MDD, and 42 healthy controls (HCs). Graph theory-based source-level weighted functional networks were assessed via strength, clustering coefficient (CC), and path length (PL) in six frequency bands. At the global level, patients with BD and MDD showed higher strength and CC, and lower PL in the high beta band, compared to HCs. At the nodal level, compared to HCs, patients with BD showed higher high beta band nodal CCs in the right precuneus, left isthmus cingulate, bilateral paracentral, and left superior frontal, belonging to the default-mode network (DMN); however, patients with MDD showed higher nodal CC only in the right precuneus compared to HCs. Although both MDD and BD patients had similar global level network changes, they had different nodal level network changes in DMN-related regions. Our findings might suggest more altered network in the DMN-related regions in patients with BD than in those with MDD.