Ammonia (NH3) concentrations in confined layer hen houses are the highest among buildings of different animal species and are of great concern to indoor air quality and animal welfare. However, little has been done to investigate the dynamic relationships between NH3 concentrations and the influencing factors. A Distributed Lag Non-linear Model was applied to study the dynamics of NH3 in two high-rise layer houses using a two-year dataset, compiled with hourly data, and its two subsets of summer and winter. Three major influencing factors, the ventilation rate, outdoor temperature, and outdoor relative humidity, were identified to have lagged effects on indoor NH3 concentrations in both houses. The duration of lagged effects of ventilation rate ranged from non-observable (<1 h) to a few subsequent hours. However, in winter, the changes in ventilation rates within the low operational ranges were not sufficiently high to induce NH3 concentration changes. The effects of temperature were not observable in winter. Higher outdoor relative humidity was related to elevated NH3 concentrations in winter, with a lag time of about 1 h in both houses. The lagged effects were considerably different between summer and winter for all three influencing factors.