The Middle East Respiratory Syndrome coronavirus is considered a deadlier but less-transmissible cousin of the SARS virus that erupted in Asia in 2003 and infected 8,273 people, nine percent of whom died.
Jordan reported the first death from MERS in February, after two fatalities in 2012.
"The new death from the coronavirus was one of those infected with the virus who was 56 years old who was suffering from anaemia and pneumonia, and who had been hospitalised," health ministry official Mohammad Abdallat was quoted as saying by state news agency Petra.
MERS emerged in 2012 and is mostly focused on Saudi Arabia, where it has killed 115 people, according to health officials there.
Saudi Arabia's number of MERS infections has also reached 414, the world's highest tally, the ministry reported.
There are no vaccines or antiviral treatments for MERS, a disease with a mortality rate of more than 40 percent that experts are still struggling to understand.
Some research has suggested that camels are a likely source of the virus.