Uncertainty is prevalent in robotics. Due to measurement noise and complex dynamics, we cannot estimate the exact system and environment state. Since conservative motion planners are not guaranteed to find a safe control strategy in a crowded, uncertain environment, we propose a density-based method. Our approach uses a neural network and the Liouville equation to learn the density evolution for a system with an uncertain initial state. We can plan for feasible and probably safe trajectories by applying a gradient-based optimization procedure to minimize the collision risk. We conduct motion planning experiments on simulated environments and environments generated from real-world data and outperform baseline methods such as model predictive control and nonlinear programming. While our method requires offline planning, the online run time is 100 times smaller compared to model predictive control.