In the following paper, we present a consistent Newton–Schur (NS) solution approach for variational multiscale formulations of the time‐dependent Navier–Stokes equations in three dimensions. The main contributions of this work are a systematic study of the variational multiscale method for three‐dimensional problems and an implementation of a consistent formulation suitable for large problems with high nonlinearity, unstructured meshes, and non‐symmetric matrices. In addition to the quadratic convergence characteristics of a Newton–Raphson‐based scheme, the NS approach increases computational efficiency and parallel scalability by implementing the tangent stiffness matrix in Schur complement form. As a result, more computations are performed at the element level. Using a variational multiscale framework, we construct a two‐level approach to stabilizing the incompressible Navier–Stokes equations based on a coarse and fine‐scale subproblem. We then derive the Schur complement form of the consistent tangent matrix. We demonstrate the performance of the method for a number of three‐dimensional problems for Reynolds number up to 1000 including steady and time‐dependent flows. Copyright © 2009 John Wiley & Sons, Ltd.