The quantification of ammonia (NH3) emissions is still a challenge and the corresponding emission factor for grazed pastures is uncertain. This study presents NH3 emission measurements of two pasture systems in western Switzerland over the entire grazing season 2016. During the measurement campaign, each pasture system was grazed by 12 dairy cows in an intensive rotational management. The cow herds on the two pastures differed in the energy to protein balance of the diet. NH3 concentrations were measured upwind and downwind of a grazed sub plot with line integrating open path instruments that were able to retrieve small horizontal concentration differences (< 0.2 µg NH3 m-3). The NH3 emission fluxes were calculated by applying a backward Lagrangian Stochastic (bLS) dispersion model to the difference of paired concentration measurements and ranged from 0 to 2.5 µg N-NH3 m-2 s-1. The fluxes increased steadily during a grazing interval from previous non-significant values to reach maximum emissions at the end of the grazing interval. Afterwards they decreased exponentially to near zero values within 3-5 days. A default emission curve was calculated for each of the two systems and adopted to each rotation in order to account for missing data values and to estimate inflow disturbances due to grazing on upwind paddocks. Dung and cow location were monitored to account for the non-negligible inhomogeneity of cow excreta on the pasture. The average emission (± std. dev. of individual rotation values) per grazing hour was calculated as 0.64 ± 0.11 g N-NH3 cow-1 h-1 for the herd with the N balanced diet (system M) and 1.07 ± 0.06 g N-NH3 cow-1 h-1 for the herd with the protein rich grass-only diet (system G). Surveys of feed intake, body weight and milk yield of the cow herds were used to estimate the nitrogen (N) excretion by an animal N budget model. Based on that, mean relative emission factors of 6.4 ± 2.0 % and 8.7 ± 2.7 % of the applied urine N were found for the systems M and G, respectively. The results can be used to validate the Swiss national emission inventory and demonstrate the positive effect of a N-balanced diet on pasture NH3 emission.