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Inadequate sanitation has been found to be a major problem in primary schools and now asUniversal Primary Education (UPE) begins to offload pupils into the secondary school system,the same problem might begin to affect secondary schools. This study, therefore, sets out toinvestigate sanitation management at Bassajjabalaba Secondary School Bushenyi District inIshaka Municipality. The required information was gathered using four methods namely, indepthinterviews, surveys, focus group discussions, and observation. Two categories ofrespondents were used including head teachers and students. It was found that although thesampled secondary school on a variety of sanitation facilities, there is generally inadequatecoverage of sanitation facilities at the school, and the phenomenon is exacerbated by theever-increasing student population due to increasing enrolment for secondary educationresulting from Universal Primary Education. The cleanliness of the available sanitationfacilities is not at its best and this forms part of the reasons why some students ignore usingfacilities and instead opt for use of bushes around the school. It was recommended that thereis a need to develop sanitation programs under which the challenge should be tackled rightfrom the root rather than attempting to manage the resultant consequences. Schooladministrations need to prioritize the aspect of sanitation and hygiene