Flood vulnerability assessment (FVA) is significant for application to address flood risks in both rural and urban areas in Malawi. Nevertheless, there is lack of FVA framework for application in urban and rural areas. The main purpose of this study was to develop flood vulnerability assessment framework through a comparative study of Lilongwe City and Karonga District in Malawi. Vulnerability was explored through a combination of underlying vulnerability factors (UVFs)-physical-social-economic-environmental and cultural with vulnerability components (VCs)-exposure-susceptibility and resilience. The UVFs and VCs were agglomerated using binomial multiple logit regression model, and Multiple Correspondence Analysis (MCA). The results reveals that except cultural-susceptibility factors (CSFs), all the agglomerated factors contribute to flood vulnerability in Karonga district (KD) and Lilongwe city (LC). The results further show that all the indicator variables in LC have a inertia value at the expected rate of less than 10% while in KD lack of credit unions (0.103), lack of markets (0.499) poverty (0.123) and (0.203); display values that deviate from the expected score of <10%. The study concludes that there are various causes of household flood vulnerability. The study recommends that a FVA framework is required that can promote resilience of communities to mitigate flood risks and support planning and decision making process in flood risk management.