Uncertainty analysis of greenhouse gas (GHG) emissions is becoming increasingly necessary in order to obtain a more accurate estimation of their quantities. The Monte Carlo simulation (MCS) and non-parametric block bootstrap (BB) methods were tested to estimate the uncertainty of GHG emissions from the consumption of feedstuffs and energy by dairy cows. In addition, the contribution to variance (CTV) approach was used to identify significant input variables for the uncertainty analysis. The results demonstrated that the application of the non-parametric BB method to the uncertainty analysis, provides a narrower confidence interval (CI) width, with a smaller percentage uncertainty (U) value of the GHG emission model compared to the MCS method. The CTV approach can reduce the number of input variables needed to collect the expanded number of data points. Future studies can expand on these results by treating the emission factors (EFs) as random variables.