Lowering the output noise of short-pulse lasers has been a long-standing effort for decades. Modeling the noise performance plays a crucial role in isolating the noise sources and reducing them. Modeling to date has either used analytical or semianalytical implementation of dynamical methods or Monte Carlo simulations. The former approach is too simplified to accurately assess the noise performance in real laser systems, while the latter approach is too computationally slow to optimize the performance as parameters vary over a wide range. Here, we describe a computational implementation of dynamical methods that allows us to determine the noise performance of a passively mode-locked laser within minutes on a desktop computer and is faster than Monte Carlo methods by a factor on the order of 10^3. We apply this method to characterize a laser that is locked using a fast saturable absorber—for example, a fiber-based nonlinear polarization rotation device—and a laser that is locked using a slow saturable absorber—for example, a semiconductor saturable absorbing mirror.