In regions like Nepal, characterized by diverse geography, missing weather data poses a significant challenge for traditional imputation methods. These methods often struggle to capture the complexities of dynamic environments adequately. To overcome this challenge, our study explores the application of graph neural networks for weather prediction in data-scarce environments. Our approach entails the development of specialized models tailored to accommodate the non-Euclidean topology inherent in weather data. This framework encompasses preprocessing, graph representation, feature selection, and imputation techniques to predict missing atmospheric variables. The adaptability of our models to intricate geography ensures more precise representations of weather conditions. Our research demonstrates the efficacy of these models through rigorous testing on a substantial dataset spanning four decades since 1981. By harnessing state-of-the-art graph neural network technology, our study aims to address existing gaps in weather data prediction, leading to improved historical weather forecasting accuracy. Ultimately, this advancement contributes to enhanced meteorological understanding and forecasting precision in data-scarce regions.