We present a full stochastic description of the pair approximation scheme to study binary-state dynamics on heterogeneous networks. Within this general approach, we obtain a set of equations for the dynamical correlations, fluctuations and finite-size effects, as well as for the temporal evolution of all relevant variables. We test this scheme for a prototypical model of opinion dynamics known as the noisy voter model that has a finite-size critical point. Using a closure approach based on a system size expansion around a stochastic dynamical attractor we obtain very accurate results, as compared with numerical simulations, for stationary and time-dependent quantities whether below, within or above the critical region. We also show that finite-size effects in complex networks cannot be captured, as often suggested, by merely replacing the actual system size N by an effective network dependent size N eff.