We reveal stacking-induced strong coupling between atomic motion and interlayer excitons through photocurrent measurements of WSe$_2$/MoSe$_2$ heterojunction photodiodes. Strong coupling manifests as pronounced periodic sidebands in the photocurrent spectrum in frequency windows close to the interlayer exciton resonances. The sidebands, which repeat over large swathes of the interlayer exciton photocurrent spectrum, occur in energy increments corresponding directly to a prominent vibrational mode of the heterojunction. Such periodic patterns, together with interlayer photoconductance oscillations, vividly demonstrate the emergence of extraordinarily strong exciton-phonon coupling - and its impact on interlayer excitations - in stack-engineered van der Waals heterostructure devices. Our results establish photocurrent spectroscopy as a powerful tool for interrogating vibrational coupling to interlayer excitons and suggest an emerging strategy to control vibronic physics in the solid-state.