Bay of Bengal (BoB) is one of the most cyclone prone regions in the world. Cyclones receive energy from warm ocean surface waters and the change in cyclone activity generally depends on the change in heat energy available in the upper ocean. Here, we use satellite‐based Modern Era Retrospective‐analysis for Research and Applications dataset, and reanalysis of Simple Ocean Data Assimilation (SODA) and European Centre for Medium‐range Weather Forecasts–Ocean ReAnalysis System 4 (ECMWF–ORAS4) to analyse the oceanic heat content (OHC) and heat flux to identify sources of the additional heat input in the region during the period 1980–2014. It has been observed that during 1999–2014, heat energy is mainly stored in the southern and northwestern parts of the bay and it shows an increasing trend in both regions. In the analysis of OHC, the European Centre for Medium‐range Weather Forecasts (ECMWF) data show a trend of −0.87 × 1018 J/month during 1980–1998 and 7.58 × 1018 J/month during 1999–2014 whereas, the SODA data show a trend of 0.94 × 1018 J/month during 1980–1998 and 5.25 × 1018 J/month during 1999–2014. It is found that many cyclones are seeded in the southeastern bay and intensified over the northwestern bay, consistent with the increase in cyclone heat potential and the upper ocean heat content (UOHC) in those regions. The heat flux in the bay is primarily governed by the heat entering the eastern side and leaving through the western side. In 1999–2014, the incoming heat flux along the eastern boundary has increased significantly (from 0.18 × 1012 to 0.57 × 1012 W/month), indicating that more heat enters the region. Furthermore, a significant reduction in the outgoing heat flux along the western boundary has also been found from the analysis. These processes trap the heat and thereby contributing to the increase in OHC in the bay. The heat flux through the bay is mainly linked with conditions prevailing over Pacific Ocean, such as, the heat influx of BoB decreases during El‐Nino and increases during La‐Nina years.