Glaciers and climate are known to exhibit positive feedbacks that are important for comprehending the overall glacier state. This relation is poorly understood in the relatively unexplored terrain like the Zanskar Himalaya. We have studied the impact of climate change regarding the past and present response of the Pensilungpa Glacier (PG), Zanskar Himalaya. Reconstructing the recent changes in the mass balance (2016–2019) along with the Little Ice Age (LIA) extent of the PG shows that the PG was joined by the five tributary glaciers during the LIA having an area of ~ 18 km2 and extended ~ 3 km downstream from its present-day snout located at 4470 ± 1 m.a.s.l. Since the LIA, the PG has retreated ~ 2941 ± 75 m, at an average rate of 5.6 ± 0.15 m a−1. Field observations for the last 4 years (2015–2019) show that the glacier now is retreating by ~ 27 ± 11 m at an average rate of 6.7 ± 3 m a−1, which is similar to the one since the LIA. The glaciers in the study area (Suru River valley) are mostly nourished by the Western Disturbances (during the December, January, and February) with maximum solid precipitation, and melt during the ablation period (May–October). The observed recessional trends of the PG may, therefore, be attributed to an increase in the temperature and decrease in precipitation during accumulation period. The ablation data reveal the significant influence of debris-cover on the mass balance and terminus retreat of the PG. Furthermore, the mass balance data for the last 3 years (2016–2019) show a negative trend with a small accumulation area ratio (AAR) (43%). The average net annual mass balance is estimated to be ~ − 3.67 × 106 m3 w.e. a−1 with the − 0.36 m w.e. a−1 specific balance between 2016 and 2019. During the period 2016–2019, the PG has lost ~ 11.03 × 106 m3 w.e. ice volume. The slower retreat rate and low AAR of the PG, compared to other glaciers in the area, suggest that its terrain characteristics (hypsometry, size, aspect, and slope) control the glacier dynamics and the glacier continues to adjust geometrically in response to the negative mass balance.