The Karoon River Basin, with an area of about 67,000 km2, is located in the southern part of Iran and has a complex mountainous terrain. No comprehensive study has been done on the spatial and temporal variations of snow cover in this region to date. In this paper, daily snow data of Moderate Resolution Imaging Spectroradiometer MODIS Terra (MOD10A1) and MODIS Aqua (MYD10A1) were examined from 1 January 2003 to 31 December 2015, to analyze snow cover variations. Due to difficulties created by cloud cover effects, it was crucial to reduce cloud contamination in the daily time series. Therefore, two common cloud removal methods were applied on the daily data. The results suggested that in winter nearly 43% of the Basin’s area experienced a negative trend, while only 1.4% of the Basin had a positive trend for snow-covered days (SCD); trends in fall and spring were less evident in the data. Using a digital elevation model of the Basin, the trends of SCD in 100 m elevation intervals were calculated, indicating a significant positive trend in SCD during the fall season above 3500 m.