The balance between neural excitation and inhibition (EIB) is an essential mechanism underlying cognitive processes. Yet, little is understood about how EIB shifts with cognitive load and its impact on functional connectivity dynamics. We investigate temporal profiles of the reciprocal modulation between EIB and functional network dynamics during working memory tasks. Notably, prefrontal EIB kinetics correlated with cognitive load, impacting stability of networks crucial for cognitive function. We observe that imbalances favouring excitation may hinder cognitive adaptability. Importantly, this experimental approach demonstrates a link between EIB kinetics, brain network dynamics and cognitive performance, defining the groundwork for exploring healthy and aberrant cognitive states.