BackgroundThe vast majority of malaria deaths in Uganda occur in children five and under and in rural areas. This study’s exploratory case study approach captured unique situations to illustrate special attributes and aspects of treatment-seeking during a malaria episode.MethodsDuring August 2010, a qualitative exploratory study was conducted in seven of Butaleja District’s 12 sub-counties. Multiple case study methodology consisting of loosely-structured interviews were carried out with eight caregivers of children five and under in the local dialect. Caregivers were geographically distant and not known to each other. Interviews were translated into English and transcribed the same day. Data were analyzed using content analysis.ResultsOf the eight cases, children recovered fully in three instances, survived but with deficits in three, and died in two. Common to all outcomes were (1) triggers to illness recognition, (2) similar treatment sequences and practices, (3) factors which influenced caregivers’ treatment-seeking decisions, (4) challenges encountered while seeking care at public health facilities, (5) cost burdens associated with managing malaria, (6) life burdens resulting from negative outcomes from malaria, (7) variations in caregiver knowledge about artemisinin combination therapy, and (8) varying perspectives how malaria management could be improved.ConclusionsDespite the reality that caregivers in Butaleja District generally share similar practices, experiences and challenges, very few children ever receive treatment in accordance with the Uganda’s national guidelines. To bring national practice into conformance with policy, three advances must occur: (1) All key stakeholders (those affiliated with the formal health system - public facilities and licensed private outlets, unlicensed drug vendors, and caregivers of young children) must concur on the need and the means to improve malaria management, (2) all health providers (formal and unlicensed) need to be engaged in training and certification to improve timely access to affordable treatment irrespective of a region’s remoteness or low population density, and (3) future public health interventions need to improve caregivers’ capacity to take the necessary actions to best manage malaria in young children.Electronic supplementary materialThe online version of this article (doi:10.1186/s12889-016-2813-7) contains supplementary material, which is available to authorized users.