Abstract This paper presents a novel methodology utilizing physics-informed neural network (PINN) as a junction condition for a 1D network model of blood flow in total cavopulmonary connection generated by the Fontan procedure. The technique integrates a 3D mesh generation process based on the parameterization of the junction geometry, along with a sophisticated physically regularized neural network architecture. Synthetic datasets are produced using 3D steady Stokes simulations within fixed boundaries. We use a physically informed feedforward neural network that utilizes a physically regularized loss function, which incorporates the principle of mass conservation. Our PINN achieves a tolerance of 6% on the test set. We develop a 1D-PINN multiscale model based on a previously developed method for multiscale 1D–3D simulations. Comparison with 1D–3D Stokes based model and 3D Navier–Stokes based model verifies the 1D-PINN model. In the first and second comparison, the maximum deviations of the averaged pressures and flows do not exceed 1.48% and 12.26%, respectively.