Drug resistance has been identified as one of the factors that lead to severe malaria and high mortality as observed in malaria endemic areas. The main objective of this study was to establish the factors that contribute to essential drug resistance in the treatment of malaria in Rachuonyo District, Kenya. Qualitative and quantitative data were collected among 380 respondents including health care providers, people seeking malaria treatment and Community Own Resource (CORPs), from 47 registered health facilities. The study revealed that all health facilities were using general-purpose trucks to transport antimalarial drugs and did not have functional wall thermometers and that eighty seven per cent (87%) of health care providers did not check storage conditions of drugs upon reception. Ninety seven per cent (97%) of the health care providers used physical examination for clinical diagnoses that is subject to errors that may lead to irrational drug use. Thirteen per cent (13%) of health care providers had no idea that antimalarials suspensions can undergo fermentation when not properly stored. Forty percent (40%) of the selected health facilities had current recommended antimalarial treatment drugs in stock. The use of such vehicles can affect the potency of the drugs, as they do not have the necessary equipments to control adverse temperatures and this may contribute to loss of potency. Some health facilities did not have the current recommended antimalarial drugs in stock implying that patients attending treatment in these facilities could have been treated with less effective drugs or they could have been sent to purchase them yet they are expensive and not easily available. In conclusion the results of this study indicate that management, administrative factors and policy issues could be a leading cause of antimalarial drug resistance and a case control study to explore the exact extent of drug resistance in this population in relation to the identified factors is urgently recommended.