The United Nation's Sustainable Development Goals include the target of ensuring access to water and sanitation and hygiene (WASH) for all; however, very few studies have assessed comprehensive school WASH service in Pakistan. The purpose of this study was to identify WASH services in primary schools of Pakistan, and to assess how recent WASH interventions and policies are associated with the school's academic performance. A representative cross-sectional study was conducted in primary schools in the Sindh province of Pakistan. Structured observations and interviews were done to ascertain the schools' WASH conditions. The primary exposures of interest were the implementation of previous WASH interventions and National WASH policy in the school and the WASH coverage. Outcomes of interest included WASH conditions and school performance. The structural equation modeling (SEM) using a bootstrap resampling procedure was employed to characterize how WASH exposures were associated with WASH conditions and school performance. Data were collected from 425 schools. The Basic WASH facilities coverage in the primary schools of Sindh remains overall low according to WHO WASH service ladder criteria. Also, inconsistency in all three inclusive domains of WASH (availability, accessibility, and functionality) facilities were found. The school performance was significantly associated (P<0.001) with the presence of WASH interventions and/or WASH policy, while WASH policy and/or recent WASH intervention at the school were not associated with overall water quality. Our assessment unveiled several WASH gaps that exist, including high heavy metal and fecal contamination. Adoption of national WASH policy and financing of evidence-based WASH interventions are recommended in primary schools to improve educational outcomes.