Decreases in pan evaporation (E_pan) over the last decades have been reported in many regions of the world. In this study, changes of E_pan in the Zoige Plateau alpine wetland (hereinafter referred to as “Zoige wetland”) and its peripheral regions from 1969 to 2014 were investigated using the PenPan model based on the long-term meteorological data. The contribution of climate factors to E_pan change were quantified by using partial derivatives of the PenPan model. Results indicated that E_pan in Zoige wetland exhibited an obvious decreasing trend before 1989, but rapidly increased after 1990. The increase in E_pan in the Zoige wetland is more significant than that in its peripheral regions and the entire Tibetan Plateau, which contributed to the more significant warming in the Zoige wetland. The pan evaporation in Zoige wetland after 1990 could be mostly attributed to changes in the aerodynamic component, and the decreasing radiation and wind speed is the primary contributor to the decline of pan evaporation during 1969–1989, while increasing air temperature and vapor pressure deficit were the major contributors to the increase of pan evaporation after 1990.