This study investigates the recent changes in natural hazard prioritizations in northern Bangladesh and presents community-based risk analyses of the various natural hazards that present threats to sustainable agriculture. The study area in northern Bangladesh included two union council areas under the Panchagarh sub-district. Climatological data analysis, a detailed questionnaire survey, and focus group discussions were conducted to assess farmers’ perceptions regarding the shifting and identification of hazards, their seasonal variation, and hazard prioritizations. The SMUG (seriousness, manageability, urgency, and growth) and FEMA (Federal Emergency Management Agency) models were applied for hazard prioritization. Hailstorms were found to be the most prioritized hazard over droughts and flash floods as perceived by the community. The farmers’ perceptions as evaluated through a questionnaire survey also support the findings of the SMUG and FEMA models. This was the first attempt to analyze the potential of hailstorms as a significant hazard in Bangladesh, and GIS maps showed their spatial distribution and temporal frequency across Bangladesh. This newly identified hazard is significantly diminishing farmers’ motivation to continue farming and has the potential to affect sustainable agriculture. The farmers’ perceptions, historical data analysis, use of the two models, institutional approach, hazard risk assessment, and vulnerability to the major sectors show that hailstorms should be considered as an important hazard in northern Bangladesh, and policymakers should pay urgent attention to minimize the threat to sustainable agriculture in northern Bangladesh.