High Mountain Asia (HMA) has the largest expanse of snow outside of the polar regions and it plays a critical role in climate and hydrology. In situ monitoring is rare due to terrain complexity and inaccessibility, making remote sensing the most practical way to understand snow patterns in HMA despite relatively short periods of record. Here, trends in snow cover duration were assessed using MODIS between 2002 and 2017 across the headwaters of the region’s primary river basins (Amu Darya, Brahmaputra, Ganges, Indus, and Syr Darya). Data limitations, associated with traditional binary mapping and data gaps due to clouds, were addressed with a daily, spatially and temporally complete, snow cover product that maps the fraction of snow in each pixel using spectral mixture analysis. Trends in fractional snow cover duration (fSCD) were calculated at the annual and monthly scale, and across 1,000 m elevation bands, and compared to trends in binary snow cover duration (SCD). Snow cover is present, on average, for 102 days across all basin headwaters, with the longest duration in western basins and shortest in eastern basins. Broadly, snow cover is in decline, which is most pronounced in elevation bands where snow is most likely to be present and most needed to sustain glaciers. Some of the strongest negative trends in fSCD were in the Syr Darya, which has 13 fewer days between 4,000–5,000 m, and Brahmaputra, which has 31 fewer days between 5,000–6,000 m. The only increasing tendency was found in the Indus between 2,000 and 5,000 m. There were differences between fSCD and SCD trends, due to SCD overestimating snow cover area relative to fSCD.