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.
Read MoreMERS: What you need to know
Isolated cases cropped up in Asia before South Korea recorded the biggest number in an outbreak that started in May.
Nearly 180 people have been infected and 27 people have died in South Korea, the largest outbreak outside Saudi Arabia. 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.