Abstract An efficient parallel algorithm for the time dependent incompressible Navier–Stokes equations is developed in this paper. The time discretization is based on a direction splitting method which only requires solving a sequence of one-dimensional Poisson type equations at each time step. Then, a spectral-element method is used to approximate these one-dimensional problems. A Schur-complement approach is used to decouple the computation of interface nodes from that of interior nodes, allowing an efficient parallel implementation. The unconditional stability of the full discretized scheme is rigorously proved for the two-dimensional case. Numerical results are presented to show that this algorithm retains the same order of accuracy as a usual spectral-element projection type schemes but it is much more efficient, particularly on massively parallel computers.