In 2016, the World Health Organization (WHO) estimated that approximately 4.2 million premature deaths worldwide were attributable to exposure to particulate matter 2.5 μm (PM2.5). This study assessed the environmental burden of disease attributable to PM2.5 at the national level in Malaysia. We estimated the population-weighted exposure level (PWEL) of PM10 concentrations in Malaysia for 2000, 2008, and 2013 using aerosol optical density (AOD) data from publicly available remote sensing satellite data (MODIS Terra). The PWEL was then converted to PM2.5 using Malaysia's WHO ambient air conversion factor. We used AirQ+ 2.0 software to calculate all-cause (natural), ischemic heart disease (IHD), stroke, chronic obstructive pulmonary disease (COPD), lung cancer (LC), and acute lower respiratory infection (ALRI) excess deaths from the National Burden of Disease data for 2000, 2008 and 2013. The average PWELs for annual PM2.5 for 2000, 2008, and 2013 were 22 μg m-3, 18 μg m-3 and 24 μg m-3, respectively. Using the WHO 2005 Air Quality Guideline cut-off point of PM2.5 of 10 μg m-3, the estimated excess deaths for 2000, 2008, and 2013 from all-cause (natural) mortality were between 5893 and 9781 (95 % CI: 3347–12,791), COPD was between 164 and 957 (95 % CI: 95–1411), lung cancer was between 109 and 307 (95 % CI: 63–437), IHD was between 3 and 163 deaths, according to age groups (95 % CI: 2–394) and stroke was between 6 and 155 deaths, according to age groups (95 % CI: 3–261). An increase in estimated health endpoints was associated with increased estimated PWEL PM2.5 for 2013 compared to 2000 and 2008. Adhering the ambient PM2.5 level to the Malaysian Air Quality Standard IT-2 would reduce the national health endpoints mortality.