Initiation of specific antimalarial treatment within 24 hrs of fever onset at home and before presentation to the hospital is one of the strategies to reduce mortality from malaria in sub-Saharan Africa. In order to determine whether this strategy is being implemented we describe the use and factors associated with the use of pre-hospital medications among children admitted with malaria in one of the tertiary hospitals in Uganda. Use of pre-hospital medications was assessed in 205 children aged 6-59 months and diagnosed with malaria at admission in Mulago hospital. Data were obtained on the type, source, and dose adequacy of medicines used before presentation to the hospital as well as the socio-demographical characteristics of the children. The proportion of children using pre-hospital medication was determined and logistic regression analysis used to determine factors associated with use of pre-hospital medication. Overall, 147/205 (72%) of the children were given some medication for their illness before presentation to the hospital. The common pre-hospital medicines used were paracetamol (107/147, 72.8 %) and antimalarial medicines (91/147, 61.9 %). Antibiotics were used in only 12 (8.2 %) of the cases. The majority (62/91, 68%) of the cases got medicines from a health facility but only 41/91 (45%) received an adequate dose. Having fever for more than three days was significantly associated with use of pre-hospital medicines (OR = 2.2; 95% CI 1.12-4.35; p = 0.02). The pre-hospital use of medicines is common amongst children presenting with malaria to this tertiary Ugandan hospital. The practice is, however, associated with use of inadequate doses of antimalarials and delay in presentation to the hospital. More effort is therefore needed to educate communities on the importance of proper home management of malaria.