Globally, a large amount of methane (CH4) emission is generated from agricultural systems including rice farming in many Asian countries including Bangladesh. However, a reliable estimate of CH4 emission from rice cultivation is not available, particularly considering the different rice types (i.e., local land races, high yielding varieties (HYV), and hybrid varieties) grown under diverse conditions. Here, we estimated current and future CH4 emission (both rate and amount) from different rice farming systems in Bangladesh using the IPCC Tier1 method. Model based estimates were validated with a pilot survey and with other studies. Across all rice types grown in different seasons, (i.e., Aus from March to August, Aman from July to December and Boro from December to June), the estimated CH4 emission in 2020 was at 2348 Gg CH4 yr− 1 (95% CIs of 799–5628 Gg CH4 yr− 1) while a slightly higher CH4 emission was estimated at 2376 Gg CH4 yr− 1 for the year 2060 after considering a 0.5 % cultivable rice land migration to non-agricultural activities. We also found significant differences in CH4 emission rates among types of rice cultivation and growing season. Average across all seasons, the highest CH4 emission was from hybrid varieties (225 kg CH4 ha− 1 yr− 1), while the lowest (128 kg CH4 ha− 1 yr− 1) from local land races. In contrast, the same local land races showed the highest emission rates when normalized against yield. Across all rice types, the largest CH4 emission was during Aman season accounting 61% of the total annual emission. Our model-based estimates reasonably compare with survey-based estimates (r2 = 0.94, p < 0.01) and fall within one standard deviation of a log-normal distribution of measurement based CH4 emissions. Our findings, therefore, provide a deeper insight into CH4 emissions from rice cultivation systems.