Tackling coupled sets of partial differential equations (PDEs) through scientific machine learning presents a complex challenge, but it is essential for developing data-driven physics-based models. We employ a novel approach to model the coupled PDEs that govern the blood flow in stenosed arteries with deformable walls, while incorporating realistic inlet flow waveforms. We propose a low-dimensional model based on neural ordinary differential equations (ODEs) inspired by 1D blood flow equations. Our unique approach formulates the problem as ODEs in space rather than time, effectively overcoming issues related to time-dependent boundary conditions and PDE coupling. This innovative framework accurately captures flow rate and area variations, even when extrapolating to unseen waveforms. The promising results from this approach offer a different perspective on deploying neural ODEs to model coupled PDEs with unsteady boundary conditions, which are prevalent in many engineering applications.