The patient was a 44-year-old Chinese man from Wuhan, in Hubei province, where the virus was first detected.
He appeared to have been infected before arriving in the Philippines, the World Health Organization (WHO) said.
More than 300 people have died in the outbreak so far, the vast majority from Hubei. More than 14,000 people have been infected.
The US, Australia and an increasing number of other countries have barred the arrival of foreigners from China and are requiring their own citizens to be quarantined.