This study examines the dynamics of naira real exchange rate (RER) during the period 2000Q1 - 2016Q1 as well as the extent to which it deviated from its long run equilibrium path. To achieve this, we adopt the Behavioural Equilibrium Exchange Rate (BEER) model approach and incorporate the effects of an endogenously determined breakpoint in the cointegrating vector of the RER model. We found empirical support for the existence of a long-run relationship between RER and its determinants that is subject to a structural break in 2011Q1. Also, model results showed that exchange rate policy, productivity and interest rate differentials are significant determinants of real exchange rate movements. In terms of the levels of RER misalignment under different exchange rate policies considered, model results indicated that the naira was overvalued by 1.22 per cent during IFEM regime of 2000 - 2002; overvalued by 0.35 per cent during rDAS (2002 - 2006); undervalued by 0.39 per cent during wDAS (2006 - 2013) and undervalued by 0.25 per cent in the period succeeding the wDAS till March, 2016. Overall, the naira was found to be overvalued by 0.15 per cent during the sample period, implying a subsidy of 0.15 kobo per dollar.