The outbreak of the COVID-19 pandemic and the subsequent global economic shutdown provided an opportunity to conduct a real-time experiment assessing the influence of global emission reductions in the Aerosol Optical Depth (AOD) level, an indicator of air pollution over Nepal. Nepal's government imposed a lockdown on the country for approximately three months (from 24 March onwards) in 2020. The purpose of this study is to examine the temporal fluctuation in Aerosol Optical Depth (AOD) caused by the COVID-19 shutdown by comparing its value during the same time period of the past year over two sites: Pokhara and Kyanjin Gompa. We comparatively analyzed the variation of diurnal mean and monthly average AOD of two selected sites, from the month of January to May 2020 and January to May 2018. By examining the time-series graph of daily average AOD prior to and during the lockdown period, our study showed an apparent fluctuation in AOD throughout the studied areas. The major findings of the research revealed that after the lockdown, a significant variation in monthly averaged AOD was observed, ranging from 20–60% deviation over Pokhara and 25–50% deviation in Kyanjin Gompa at different wavelengths. This confirms previous studies on aerosols and other particulate matter during COVID-19 lockdown, as well as theoretical assumptions. In addition, we performed the heatmap correlation analysis among AOD, Total precipitable water (Tpw), Angstrom exponent (α), Turbidity coefficient (β), and Visibility (V) during the studied period with possible explanations. We believe this research work serves as a crucial reference for our government to implement appropriate policies for pollution control over the studied areas in the future.