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National malaria treatment policies are devised to guide health professionals and to facilitate diagnosis and case management. Following the recommendations of the WHO, Cameroon changed its malaria treatment policy from monotherapy to artemisinin-based combination therapy (ACT) as the first-line treatment for uncomplicated malaria. We report an investigation into trends of case management following this change in policy. Data was collected retrospectively, through consultation and perusal of laboratory and prescription registers of the Mbakong Health Centre. Analysis of data was done using SPSS and SAS Statistics. Data presented herein demonstrate that from 2006 to 2012, a total of 2484 (58.7%) of the total prescriptions included an anti-malarial, 1989 (47.0%) included an antibiotic and 1935(45.7%) included an antipyretic. The anti-malarials prescribed were Anti-malaria combination therapy (ACT) – 1216 (47.6%), quinine 1044 (40.8%) or SP 296 (11.6%). Of the 1216 patients prescribed an ACT, 441(36.3%) had a positive malaria parasite confirmation, 746 (61.3%) were negative for plasmodium. Overall, 29 patients (2.4%) were treated either with an ACT without any test performed. Quinine intake was recorded in 566 (54.2%) patients positive for plasmodium. ACT prescription increased from 23% in 2007 to between 44 and 45% in 2008–2009. During this period there was a corresponding drop in the prescription of quinine from 38% in 2007 to 13% in 2009 (r = −0.43, p > 0.05). Sulphadoxine-Pyrimethamine (SP) was restrictively prescribed to women of childbearing age (97.0%) after 2008. Antibiotics prescription dropped from 53.7% to 39.3% from 2010 to 2012. The odds of being prescribed an antibiotic was significantly higher in patients with a malaria negative result compared to malaria positive patients (OR = 6.12, CI 4.74–7.91, p < 0.00001). Overall, there is an over treatment of malaria, thus departing from the WHO guidelines of appropriate treatment. Although there is an overall increase in the prescription of ACT, less prescription of quinine and a noticeable restrain from prescription of SP to febrile cases, the old practice was still rampant. There is need for healthcare workers to adhere to guidelines in order to enhance the rational use of drugs to achieve appropriate treatment of uncomplicated malaria according to WHO guidelines DST/NWU Preclinical Drug Development Platform of the North-West University, the Division of Research,Catholic University of Cameroon Bamenda, the Research Office of the North-West University, Potchefstroom, South Africa, the Laboratory of Public Health Research Biotechnologies and the Njongdong Foundation