This work applies resolvent analysis to incompressible flow through a rectangular duct, in order to identify dominant linear energy-amplification mechanisms present in such flows. In particular, we formulate the resolvent operator from linearizing the Navier–Stokes equations about a two-dimensional base/mean flow. The laminar base flow only has a nonzero streamwise velocity component, while the turbulent case exhibits a secondary mean flow (Prandtl’s secondary flow of the second kind). A singular value decomposition of the resolvent operator allows for the identification of structures corresponding to maximal energy amplification, for specified streamwise wavenumbers and temporal frequencies. Resolvent analysis has been fruitful for analysis of wall-bounded flows with spanwise homogeneity, and here we aim to explore how such methods and findings can extend for a flow in spatial domains of finite spanwise extent. We investigate how linear energy-amplification mechanisms (in particular the response to harmonic forcing) change in magnitude and structure as the aspect ratio (defined as the duct width divided by its height) varies between one (a square duct) and ten. We additionally study the effect that secondary flow has on linear energy-amplification mechanisms, finding that in different regimes it can either enhance or suppress amplification. We further investigate how the secondary flow alters the forcing and response mode shapes leading to maximal linear energy amplification.