Observation of glacier surface characteristics through remotely sensed time-series data is essential for understanding glacier seasonality, mass balance, and long-term trends. Yet, the reliability of these observations depends significantly on the quality of the time-series data. This study presents a meticulous preprocessing scheme to improve the quality of Moderate Resolution Imaging Spectroradiometer (MODIS) Normalized Difference Snow Index (NDSI) time-series data for glacier monitoring. We propose a three-step algorithm specifically crafted to overcome the challenges associated with cloud contamination reduction, outlier removal and data gap handling. This innovative approach iteratively compares the median values of automatically adjusted asymmetrical moving windows to achieve convergence, removing outliers using minimal window size to keep the temporal resolution as high as possible. The methodology’s effectiveness is demonstrated through its application to two glaciers from the United States Geological Survey (USGS) Benchmark Project, showcasing significant improvements in the quality of smoothed MODIS NDSI time series. These results affirm the efficacy of the proposed scheme in rendering a more reliable evaluation of glacier surface condition and seasonal fluctuations. Consequently, this study contributes significant methodological advancements to the fields of remote sensing and glaciology, enhancing the accuracy of glacier monitoring techniques.