Accurate nighttime land surface temperature (LSTn) forecasting in data-scarce, topographically complex regions remains a significant challenge for satellite remote sensing and climate monitoring. To address this, the present study introduces the Physics-Guided Transformer Bidirectional Long Short-Term Memory (PG-ST-BiLSTM) deep learning model. For comparison, we employ four baseline models: three deep learning models (TCN, LSTM, and BiLSTM) and one statistical model (linear regression). Using Afghanistan, a topographically challenging and data-scarce region, as a “hard” test bed, the proposed model is evaluated across five major river basins over the period 2001-2024. The proposed PG-ST-BiLSTM achieves an R² of 0.977, RMSE of 2.023 °C, and MAE of 1.534 °C, outperforming baseline models including TCN (R² = 0.961), LSTM (R² = 0.966), BiLSTM (R² = 0.966), and linear regression (R² = 0.926). The model demonstrates strong alignment between observed and fitted LSTn values along the reference line of y = 0.98x + 0.21 closely approaching the 1:1 reference line. All Sen’s slope values are positive, confirming a universal nighttime warming trend across the projected period (2025-2040), with a grand mean of +0.0160 °C/year across all basin-season combinations, suggesting a marginal acceleration of LSTn warming under a trend-stationary climatological assumption, wherein historical warming rates derived from Mann-Kendall and Theil–Sen analyses are assumed to persist through 2040. At the seasonal level, Winter exhibits the highest projected warming rate (+0.1174 °C/year), followed by Summer (+0.0984 °C/year), Autumn (+0.0545 °C/year), and Spring (+0.0504 °C/year), indicating that cold-season and peak-summer nighttime temperatures are projected to remain the most thermally vulnerable through 2040. At the basin level, the hyper-arid Helmand Basin records the highest projected mean Sen’s slope (+0.0796 °C/year), consistent with its minimal vegetation buffering and high nocturnal thermal emissivity, while the Amu-Darya Basin exhibits the lowest warming rate (+0.0460 °C/year), attributable to orographic cooling and comparatively higher soil moisture retention. These results demonstrate the generalizability and reproducibility of the PG-ST-BiLSTM model for nighttime LST forecasting in data-scarce, mountainous regions, with direct relevance to climate adaptation, water resource planning, and cryosphere monitoring worldwide.