Recent research on the effect of climate variables on coronavirus (COVID-19) transmission has emerged. Climate change can potentially cause new viral outbreaks, illness, and death. This study contributes to COVID-19 disease prevention efforts. This study makes two contributions: (1) we investigated the impact of climate variables on the number of COVID-19 cases in 34 Indonesian provinces, and (2) we developed a transformer-based deep learning model for time series forecasting for the number of positive COVID-19 cases the following day based on climate variables in 34 Indonesian provinces. We obtained data from March 15, 2020, to July 22, 2021, on the number of positive COVID-19 cases and climate change variables (wind, temperature, humidity) in Indonesia. To examine the effect of climate change on the number of positive COVID-19 cases, we employed 15 scenarios for training. The experiment results of the proposed model show that the combination of wind speed and humidity has a weakly positive correlation with positive COVID-19 incidence; however, the temperature has a considerably negative association with positive COVID-19 incidences. Compared to the other testing scenarios, the transformer-based deep learning model produced the lowest MAE of 175.96 and the lowest RMSE of 375.81. This study demonstrates that the transformer model works well in several provinces, such as