We present a numerical model for mode-locked lasers and ultrafast nonlinear amplifiers in which the saturated gain profiles along active fibers are judiciously computed using experimental pump powers as input. This eliminates the need for approximating the gain profile by using a small-signal gain coefficient and saturation energy to simulate pulse propagation in active fibers. Our model shows good agreement with experiments involving mode-locked cavities at 1 µm with a silica glass host doped with ytterbium ions. Accurate results are also obtained for continuous-wave and mode-locked laser cavities around 2.8 µm, which uses ZBLAN fiber doped with erbium ions. In the case of Er:ZBLAN fiber, we use the model to show regions of stable mode-locking delivering a single pulse as output and how the spectral width changes with variation in doping concentration and fiber lengths. Our model enables accurate numerical modeling of mode-locked fiber lasers and ultrafast amplifiers, and can be useful in guiding the design of new architectures, understanding complex intracavity laser dynamics, and optimizing device output.