An analysis method for the uncertainty of a small evaporation rate in a magnetic suspension balance/diffusion-tube humidity generator has been developed. Using experimentally obtained data, the uncertainty is evaluated as a function of measurement time. It is found that the observed standard deviation of the evaporation rate in a region of short measurement time (short term) is inversely proportional to the measurement time, and that in a region of long measurement time (long term) the standard deviation does not vary markedly with increasing measurement time. The behavior of the observed standard deviation in the short term is attributable mainly to the uncertainty of the balance reading, and that in the long term to the variability of room temperature. The results of the investigation show that the use of only least-squares analysis leads to underestimation of the uncertainty.