The global health body said the two countries have become the first in the south east Asian region (SEAR) to be verified for having interrupted endemic measles virus transmission, ahead of the 2020 regional target.
Measles is a highly infectious disease that is a major childhood killer globally.
"Bhutan and Maldives have demonstrated how a highly contagious virus like measles can be eliminated. The WHO commends them for this momentous public health achievement," Poonam Khetrapal Singh, Regional Director of WHO South East Asia, said.
Maldives has not reported any case of indigenous measles since 2009 and Bhutan since 2012.
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Measles elimination and rubella control by 2020 has been one of WHO south east Asian region's flagship priority programmes since Singh became its regional director in February 2014.
"An estimated 6,20,000 measles deaths have been averted in 2016 alone following vaccination carried out by member countries.
"Nearly 107 million children have been reached with an additional dose of measles vaccine through mass vaccination between 2013 and 2016," WHO said.
Bhutan and Maldives launched their Expanded Program on Immunization in 1979 and 1976 respectively, and worked indefatigably to increase access to immunisation services.
"Both countries achieved and maintained high coverage of measles vaccination, despite geographical challenges.
"They also established strong laboratory-supported surveillance for measles, and have conducted detailed case investigation and tracking, right up to the very last case," Singh said.
All countries are conducting case-based surveillance for measles and rubella, and regional surveillance standards have been revised to meet elimination standards.
The measles laboratory network has been expanded from 23 laboratories in 2013 to 39 WHO accredited laboratories in 2016, WHO said.
"To meet the 2020 measles elimination and rubella control goals, all countries need to make greater efforts to increase measles vaccination coverage through childhood immunisation programmes, as nearly 4.7 million children remain unvaccinated against measles in the region annually," Singh said.