Climate-sensitive diseases developing from heat or cold stress threaten human health. Therefore, the future health risk induced by climate change and the aging of society need to be assessed. We developed a prediction model for mortality due to cardiovascular diseases such as myocardial infarction and cerebral infarction, which are weather or climate sensitive, using machine learning (ML) techniques. We evaluated the daily mortality of ischaemic heart disease (IHD) and cerebrovascular disease (CEV) in Tokyo and Osaka City, Japan, during summer. The significance of delayed effects of daily maximum temperature and other weather elements on mortality was previously demonstrated using a distributed lag nonlinear model. We conducted ML by a LightGBM algorithm that included specified lag days, with several temperature- and air pressure-related elements, to assess the respective mortality risks for IHD and CEV, based on training and test data for summer 2010–2019. These models were used to evaluate the effect of climate change on the risk for IHD mortality in Tokyo by applying transfer learning (TL). ML with TL predicted that the daily IHD mortality risk in Tokyo would averagely increase by 29% and 35% at the 95th and 99th percentiles, respectively, using a high-level warming-climate scenario in 2045–2055, compared to the risk simulated using ML in 2009–2019.