Background: Botswana significantly reduced its malaria burden between 2000 and 2012. Incidence dropped from 0.99 to 0.01 % and deaths attributed to malaria declined from 12 to 3. The country initiated elimination strategies in October 2012. We examine the progress and challenges during implementation and identify future needs for a successful program in Botswana. Methods: A national, rapid notification and response strategy was developed. Cases detected through the routine passive surveillance system at health facilities were intended to initiate screening of contacts around a positive case during follow up. Positive cases were reported to district health management teams to activate district rapid response teams (DRRT). The health facility and the DRRT were to investigate the cases, and screen household members within 100 m of case households within 48 h of notification using rapid diagnostic tests (RDT) and microscopy. Positive malaria cases detected in health facilities were used for spatial analysis. Results: There were 1808 malaria cases recorded in Botswana during 26 months from October, 2012 to December, 2014. Males were more frequently infected (59 %) than females. Most cases (60 %) were reported from Okavango district which experienced an outbreak in 2013 and 2014. Among the factors creating challenges for malaria eradication, only 1148 cases (63.5 %) were captured by the required standardized notification forms. In total, 1080 notified cases were diagnosed by RDT. Of the positive malaria cases, only 227 (12.6 %) were monitored at the household level. One hundred (8.7 %) cases were associated with national or transnational movement of patients. Local movements of infected individuals within Botswana accounted for 31 cases while 69 (6.01 %) cases were imported from other countries. Screening individuals in and around index households identified 37 additional, asymptomatic infections. Oscillating, sporadic and new malaria hot-spots were detected in Botswana during the study period. Conclusion: Botswana's experience shows some of the practical challenges of elimination efforts. Among them are the substantial movements of human infections within and among countries, and the persistence of asymptomatic reservoir infections. Programmatically, challenges include improving the speed of communicating and improving the thoroughness when responding to newly identified cases. The country needs further sustainable interventions to target infections if it is to successfully achieve its elimination goal.