Seoul's health ministry cited "no further risk" of infection, about seven months after the first case was diagnosed in May.
World Health Organisation standards call for a four-week waiting period after the last MERS patient fully recovers before an outbreak can definitively be said to be over.
The virus infected 186 people, with nearly 17,000 people confined to their homes and thousands of schools temporarily closing at the peak of the largest MERS outbreak outside Saudi Arabia, where it first appeared in 2012.
The virus is considered a deadlier but less infectious cousin of Severe Acute Respiratory Syndrome (SARS), which killed hundreds of people when it appeared in Asia in 2003.
The MERS outbreak took a heavy toll on the South Korean economy, stifling consumer spending and devastating the tourist sector for months.
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