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Background: Malaria has been a major public health problem in the newly established Democratic Republic of Timor Leste with over 200,000 cases being reported in 2006 and 2007. The National Malaria Control Programme (NMCP) was established in 2003. The progress made in malaria control in Timor Leste is reported. Methods: Records maintained at the NMCP, the district health services, the Health Information and Management System, the National Laboratory on malaria diagnosis and entomological data of the NMCP were reviewed. Results: There has been a 97% decrease in the reported malaria incidence from 2006 (223,002 cases) to 2012 (6,202 cases). 185,106 clinical cases reported in 2006 decreased to 2,016 in 2012 with introduction and expansion of malaria microscopy services and introduction of monovalent RDTs in 2008 and bivalent RDTs in 2010 in all parts of the country. The National Treatment Guidelines using ACT as the first-line treatment for Plasmodium falciparum infections and introduction of monovalent RDTs, led to a 42% and a 33% decrease from 2007 to 2008 in reported clinical and total malaria cases, respectively. LLINs were distributed initially to pregnant females and children under five and later per every two persons living in high-risk areas (based on microstratification at sub-district level). IRS was carried out in three districts in 2010 and extended to six districts in 2012. Anopheles barbirostris and Anopheles subpictus have been incriminated as malaria vectors. A National Laboratory, which routinely cross checks blood smears for quality assurance of microscopy was established. Malaria focal points at regional, district and sub district level, entomology surveillance staff, monitoring and evaluation officers, and quality control technicians were appointed to strengthen malaria control activities at all levels in the country. Conclusion: The 97% decrease in the incidence of malaria in Timor Leste is due to application of evidence-based malaria control methods that included enhancing improved quality surveillance, early diagnosis and prompt treatment of cases with effective anti-malarials, targeted vector control, human resource development and deployment, commitment of staff, GFATM funding and technical assistance from WHO. [ABSTRACT FROM AUTHOR]