The 36-year-old was admitted to hospital on Saturday and was under observation, Health Ministry spokesman Lyndon Lee-suy said, adding contact tracing was now under way to prevent the spread of the disease.
The man had also travelled to Saudi Arabia, the spokesman said. His condition was improving and there was no known transmission so far.
The first case discovered in the Philippines was in January, a Filipino nurse working in Saudi Arabia who survived.
MERS was first identified in humans in Saudi Arabia in 2012 and the majority of cases have been in the Middle East. Scientists are not sure of the origin of the virus, but several studies have linked it to camels.
Isolated cases cropped up in Asia before an outbreak erupted in South Korea in May and became the largest outside of Saudi Arabia.
A total of 186 people have been infected in South Korea, and 33 have died. The country's health authorities said on Monday that the outbreak may have turned the corner, with only four new cases reported in the past week.
In the Thai capital Bangkok, more than a hundred people were believed to have been in contact with an Omani man, the only MERS case in Thailand who eventually recovered.
The World Health Organization described South Korea's outbreak as a "wake-up call" but said it did not constitute a global emergency.