Background: In 2008 the Ministry of Health (MOH) in Botswana was inspired by an overall decline of malaria prevalence within the population from 4.2% in 2000 to less than 1% in 2008. These Results motivated the government of Botswana to embark on complete elimination of malaria by 2015. Heavy rainfalls in 2017 led to an epidemic which caused a huge setback to this elimination target, due to the malaria cases reported in the South-East District, a region not classified as endemic in Botswana. This study examines the progress, effectiveness, and challenges of prevention and control methodsfor a successful elimination of malaria in Botswana. Materials and Methods: Retrospective data about cases of malaria in Botswana covering endemic districts, and data about Indoor Residual Spray (IRS), Long lasting Insecticides Nets (LLINs) and larviciding from 2000 to 2018 were obtained from the Botswana MOH. Rainfall data from the Department of Metrological Services were also obtained. Intervention datasets were compared against rainfall amount and number of cases to establish their relationship. Results: There was a direct proportion between percentage of malaria incidence and percentage of mean annual rainfall. Intensifying interventions in Botswana had no effect on number of cases based on this study. IRS coverage and intensity increased over years to 80%, yet one heavy rainfall season Resultsed in increased cases of malaria in Botswana. Conclusions: Improved forecasting can be used to predict malaria in Botswana, indicating malaria in Botswana is heavily dependent on the climate . IRS, LLINs and larviciding should be carried out at the right time, not after mosquito bites and consistently without failure, to eliminate malaria. The steep decline of cases of malaria from 2000 to 2013 was due to the dry weather, not control methodsapplied.