Abstract Among all hydrometeorological parameters, rainfall strongly correlates with hydrometeorological disasters. The rainfall forecast process remains challenging due to the nonlinear, nonstationary nature and multiscale variability of rainfall. Moreover, the unique microclimate in different regions further complicates the forecasting process. This study proposes a hybrid model employing multivariate singular spectrum analysis (MSSA) and long short-term memory (LSTM) for multistep-ahead hourly rainfall forecasting in urban areas of northeast India. The model is trained and evaluated using high-resolution (12 km) hourly meteorological data from the Indian Monsoon Data Assimilation and Analysis (IMDAA) dataset for Guwahati (plain) and Aizawl (hilly) regions from 2015 to 2019. The hybrid model outperforms the single LSTM model in both plain and hilly regions, with an average percentage gain of 47.99% and 43.88% for symmetric mean absolute percentage error (SMAPE) and root-mean-square error (RMSE) in the case of the Guwahati dataset and 84.59% and 82.27% in the case of the Aizawl dataset, respectively. The performance of the LSTM model significantly improves as the zero values in the observed data are eliminated after reconstruction by MSSA. This enables the model to discern essential patterns and relationships in the data, which leads to more accurate forecasts. However, the hybrid model underestimates the rainfall, which can be tackled by hypertuning the parameters. The study highlights the importance of considering the interplay between rainfall and meteorological parameters for accurate rainfall forecasting in urban areas. The proposed MSSA–LSTM model can be used as a decision support tool for urban planning and disaster management. Significance Statement This study addresses a critical need in multistep-ahead hourly rainfall forecasting in urban areas, with a focus on the unique conditions of northeast India. Our research has identified the presence of red noise in the rainfall data, shedding light on the complexities of the underlying rainfall patterns. Furthermore, we delve into the intricate interplay between rainfall and meteorological parameters, providing valuable insights into the factors influencing rainfall dynamics. Notably, our study underscores the region-specific challenges in rainfall forecasting. While the hybrid model demonstrates reasonable accuracy in the plains, its performance in the hilly region falls short of expectations. This highlights the nuanced nature of rainfall prediction in areas with varying topography and emphasizes the need for tailored forecasting approaches.