Abstract Computational Fluid Dynamics (CFD) has gained significant utility in the analysis of diverse fluid flow scenarios, thanks to advances in computational power. Accurate error estimation techniques are crucial to ensure the reliability of CFD simulations, as errors can lead to misleading conclusions. This study focuses on the estimation of discretization errors in time-dependent simulations, building upon prior work addressing steady-state problems Wang et al. (2020, “Error Transport Equation Implementation in the Sensei CFD Code,” AIAA Paper No. 2020-1047). In this research, we employ unsteady error transport equations (ETE) to generate localized discretization error estimates within the framework of the finite volume CFD code SENSEI. For steady-state problems, the ETE only need to be solved once after the solution has converged, whereas the unsteady ETE need to be co-advanced with the primal solve. To enhance efficiency, we adopt a one-sided temporal stencil and develop a modified iterative correction process tailored to the unsteady ETE. The time-marching schemes utilized encompass second-order accurate singly diagonally implicit Runge–Kutta (SDIRK) and second-order backward differentiation formula (BDF2), both being implicit. To rigorously assess the accuracy of our error estimates, all test cases feature known analytical solutions, facilitating order-of-accuracy evaluations. Two test cases are considered: the 2D convected vortex for inviscid flow and a cross-term sinusoidal (CTS) manufactured solution for viscous flow. Results indicate higher-order convergence rates for the 2D convected vortex test case even when iterative correction is not applied, with similar observations in the CTS case, albeit not at the finest grid levels. Although the current implementation of iterative correction exhibits lower stability compared to the primal solve, it generally enhances the discretization error estimate. Notably, after iterative correction, the discretization error estimate for the unsteady ETE achieves higher-order accuracy across all grid levels in the 2D CTS manufactured solution.