Brain networks and cognition have recently begun to attract attention: studies suggest that more efficiently wired resting-state brain networks are indeed correlated with better cognitive performance. “Small-world” brain networks combine local segregation with global integration, hereby subserving information processing. Furthermore, recent studies implicate that gender effects may be present in both network dynamics and its correlations with cognition. This study reports on the relation between resting-state functional brain topology with overall and domain-specific cognitive performance in healthy participants and possible gender differences herein. Healthy participants underwent neuropsychological tests, of which individual scores were converted to z-scores. Network analysis was performed on resting-state, eyes-closed magnetoencephalography (MEG) data, after determining functional connectivity between each pair of sensors. The clustering coefficient (local specialization), average path length (overall integration and efficiency) and “small-world index” (i.e. ratio between clustering and path length) were calculated in six frequency bands. 14 male and 14 female participants were included. Better total cognitive performance was related to increased local connectivity in the theta band, higher clustering coefficient (in delta and theta bands) and higher small-worldness (in theta and lower gamma bands). Women showed less clustering and shorter path length in the delta band. There were no significant correlations between network topology and cognitive functioning in females. In contrast, higher cognitive scores in men were associated with increased theta band clustering and small-worldness. These results provide further evidence for the value of functional brain network topology for cognitive functioning and suggest that gender is an important factor in this respect.