An efficient and expressive wave function Ansatz is key to scalable solutions for complex many-body electronic structures. While Slater determinants are predominantly used for constructing antisymmetric electronic wave function Ansätze, this construction can result in limited expressiveness when the targeted wave function is highly complex. In this work, we introduce Waveflow, an innovative framework for learning many-body fermionic wave functions using boundary-conditioned normalizing flows. Instead of relying on Slater determinants, Waveflow imposes antisymmetry by defining the fundamental domain of the wave function and applying necessary boundary conditions. A key challenge in using normalizing flows for this purpose is addressing the topological mismatch between the prior and target distributions. We propose using O-spline priors and I-spline bijections to handle this mismatch, which allows for flexibility in the node number of the distribution while automatically maintaining its square-normalization property. We apply Waveflow to a one-dimensional many-electron system, where we variationally minimize the system’s energy using variational quantum Monte Carlo (VQMC). Our experiments demonstrate that Waveflow can effectively resolve topological mismatches and faithfully learn the ground-state wave function.