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Deformable microchannels emulate a key characteristic of soft biological systems and flexible engineering devices: the flow-induced deformation of the conduit due to slow viscous flow within. Elucidating the two-way coupling between oscillatory flow and deformation of a three-dimensional (3-D) rectangular channel is crucial for designing lab-on-a-chip and organ-on-a-chip microsystems and eventually understanding flow–structure instabilities that can enhance mixing and transport. To this end, we determine the axial variations of the primary flow, pressure and deformation for Newtonian fluids in the canonical geometry of a slender (long) and shallow (wide) 3-D rectangular channel with a deformable top wall under the assumption of weak compliance and without restriction on the oscillation frequency (i.e. on the Womersley number). Unlike rigid conduits, the pressure distribution is not linear with the axial coordinate. To validate this prediction, we design a polydimethylsiloxane-based experimental platform with a speaker-based flow-generation apparatus and a pressure acquisition system with multiple ports along the axial length of the channel. The experimental measurements show good agreement with the predicted pressure profiles across a wide range of the key dimensionless quantities: the Womersley number, the compliance number and the elastoviscous number. Finally, we explore how the nonlinear flow–deformation coupling leads to self-induced streaming (rectification of the oscillatory flow). Following Zhang and Rallabandi (J. Fluid Mech., vol. 996, 2024, p. A16), we develop a theory for the cycle-averaged pressure based on the primary problem’s solution, and we validate the predictions for the axial distribution of the streaming pressure against the experimental measurements.