Snowmelt significantly contributes to meltwater in most parts of High Mountain Asia. The Karakoram region is one of these densely glacierized and snow-covered regions. Several studies have reported that glaciers in the Karakoram region remained stable or experience slight mass loss. This trend has called for further investigation to understand changes in other components of the cryosphere. This study estimates the comparative snow cover area (SCA) and snowline altitude (SLA) changes between 2003 and 2018 in the Karakoram region and its subbasins, including Hunza, Shigar, and Shyok. We used three different 8-day composite snow products of the Moderate Resolution Imaging Spectroradiometer (MODIS) in this study including (1) Original Aqua (MYD10A2), (2) Original Terra (MOD10A2), and (3) Improved Terra-Aqua (MOYDGL06*) snow products from 2003 to 2018. We used Mann–Kendall and Sen Slope methods to assess trends in the SCA and SLA. Our results show that the original snow products are significantly biased when investigating seasonal and annual trends. However, discarding a cloud cover of >20% in the original products improves the results and makes them more comparable to our improved snow product. The original products (without cloud removal) overestimate the SCA during summer and underestimate the SCA during winter and year-round throughout the Karakoram region. The bias in the mean annual SCA between improved and Aqua and Terra cloud threshold products for the Karakoram region is found to be −1.67% and 1.1%, respectively. The improved (MOYDGL06*) product reveals a statistically insignificant decreasing trend of the SCA on the annual scale between 2003 and 2018 in the Karakoram region and all three subbasins. The annual trends decreased at −0.13%, −0.1%, −0.08%, and −0.05% in the Karakoram, Hunza, Shigar, and Shyok, respectively. The monthly trends were slightly positive overall in December. The annual maximum SLA shows a statistically significant upward trend of 13 m above sea level (m a.s.l.) per year for the entire Karakoram region. This finding suggests a significant uncertainty in water resource planning based on the original snow data, and this study recommends the use of the improved snow product for a better understanding.