Torrential rainfall following the monsoon season occurs annually in Pakistan and adversely affects health service delivery and population health. This qualitative study was undertaken in five flood-prone districts to examine district health systems' performance during floods in Pakistan. The first of its kind study to gather an in-depth assessment of the capacity of district health systems in maintaining healthcare services during floods. Key informant interviews were conducted with 37 district stakeholders and 42 frontline healthcare providers. Nine focus group discussions were also conducted with 56 lady health workers. World Health Organization health systems' six building blocks framework was utilized to assess the performance of district health systems. The findings illustrated increased reporting of diseases, and domestic and sexual violence against females. The damaged roads and unavailability of transportation during floods affected outreach services in the communities. The inadequate availability of funds resulted in critical gaps in the supply chain for essential medicines and supplies, impeding outreach services. Shortage of female medical staff was reported in addition to poor attention to the training of staff for disaster response. Furthermore, reporting mechansim varied across provinces with daily reporting system of acute illnesses instituted. Moreover, district health systems lacked gender-sensitive responses in responding to flood emergencies. This study identified multiple health system constraints that resulted in poor district health systems' capacity in delivering essential healthcare services during floods. This study, therefore, highlighted a need to improve district health systems' capacity in effectively responding to healthcare service needs during floods.