Rapid increases and decreases in the synchronisation or functional coupling of neural systems are widely considered key mechanisms for the integration and segregation of neural systems in cognition. In this study, we use Steady State Visually Evoked Potential-Event Related Partial Coherence (SSVEP-ERPCOH) to investigate the relationship between such functional coupling and individual performance on the mental rotation task. Twenty-two right-handed males performed a sequential version of the mental rotation task. Brain electrical activity was recorded from 64 scalp sites and the SSVEP elicited by a diffuse 13 Hz visual flicker superimposed over the visual fields. The correlation between SSVEP-ERPCOH and speed and accuracy was determined during the intake, the hold and rotation components of the task. During the intake component, speed and accuracy were negatively correlated with pre-frontal, frontal and central SSVEP-ERPCOH. During the hold component speed and accuracy were positively correlated with right pre-frontal and frontal SSVEP-ERPCOH although this effect was stronger speed. During the subsequent rotate component, speed and accuracy were negatively correlated with left temporal SSVEP-ERPCOH. These results will be discussed in the context of the role of inhibitory processes in sculpting the dynamic interaction between neural systems in cognition.