A finite-difference time-domain (FDTD) simulation of Yb-doped cladding-pumped, mJ-level, excitation-balanced fiber pulse amplifiers (EBFAs) is presented. In EBFAs, two pumps, one above (anti-Stokes pump, or ASP) and one below (Stokes pump, or SP) the signal wavelength, are utilized to reduce the net thermal energy generated due to the quantum defect. From the results of the FDTD simulation, detailed analyses on the fiber length optimization, excited Yb3+ population evolution, pump and signal power evolution, optical-to-optical (o-o) conversion efficiency, wall plug efficiency, as well as thermal energy generation are performed. For example, with an ASP at 990 nm and a SP at 975 nm, only 2.3 µJ of thermal energy is produced when generating a 2 mJ output pulse at 985 nm, whereas a pulse amplifier with only SP pumping rendering the same 2 mJ output gives more than 10 times the thermal energy. In the meantime, the system maintains an o-o efficiency of 8.43% and wall plug efficiency of 6.6%. The results here indicate the feasibility of the power-scaling of excitation-balanced laser systems, and the FDTD model will be beneficial for the design and optimization of such systems. The first half of this paper presents the FDTD model and provides an example calculation outlining the modeling procedure. The remaining half details the impact of varying laser parameters on system performance. These include pumping and input signal energies, repetition rates, and selection of the ASP, SP, and signal wavelengths. The results presented herein can also be extended to excitation balancing in other solid-state laser systems, such as Yb:YAG and Tm:YAG lasers.