Abstract Background Neurocognitive dysfunction in bipolar disorder represents a possible marker of underlying pathophysiology, but to date, most studies are cross-sectional and heterogeneous with regard to pharmacological treatments. In the present study we investigated the 6-year cognitive and functional outcome of a sample of euthymic excellent lithium responders (ELR). Method A total sample of twenty subjects was assessed at baseline and 6 years later: ten diagnosed of bipolar disorder according to DSM-IV criteria and ten healthy matched controls. The sample size was enough to find statistical differences between groups, with a statistical power of 0.8. Bipolar patients were on lithium treatment during all this follow-up period and fulfilled ELR criteria as measured by the Alda scale. A neuropsychological test battery tapping into the main cognitive domains was used at baseline and at after 6-year of follow-up. Functional outcome was evaluated by means of the Functioning Assessment Short Test at study endpoint. Results Repeated measures multivariate analyses of variance showed that bipolar patients were cognitively impaired in the executive functioning, inhibition, processing speed and verbal memory domains (p < 0.03) compared to controls and such deficits were stable over time. Longer duration of illness and lower psychosocial outcome were significantly related to cognitive impairment (p < 0.05). Conclusions Cognitive dysfunction was present even in euthymic ELR. These deficits remain stable over the long term, and are basically associated with greater symptoms and poorer psychosocial adjustment.