Ammonia has recently been proposed as a promising candidate fuel for anion-exchange membrane fuel cell (AEMFC) technology. Direct ammonia AEMFCs (DA-AEMFCs) are a carbon-free technology that combines the ammonia’s high energy density with the fuel cells’ high efficiency. However, two major challenges face this technology: ammonia crossover (due to ammonia’s high solubility in water) and sluggish ammonia oxidation reaction (AOR). We have developed, applied, and presented a one-dimensional and transient model of a DA-AEMFC system to address these challenges. Excellent agreement is obtained between the experimentally-measured and computationally-simulated performance of DA-AEMFCs operating at 100 and 120 °C with KOH-free anode feed. As the current density increases, the initial cell performance analysis reveals a reduction in the parasitic AOR rate through the cathode. More intriguingly, the results demonstrate a positive impact of ammonia crossover on cell longevity. Crossover drives an AOR within the cathode, which has a detrimental effect on performance but comes with an associated benefit of water generation in this region. The resultant improvement in the cathode hydration reduces the degradation rate of ionomeric material, ultimately increasing cell lifetime. Further studies are required to determine the desired rate of ammonia crossover and its influence on the system’s cost-effectiveness.