Zest Air will start the service from Jan 29 using a brand new Airbus A320 aircraft, it said in a statement.
Unlike other low-fare carriers, Zest Air said it will offer free inflight meals and snacks and a baggage allowance of 30kg per passenger.
A one-way ticket for the new route will carry an introductory price of US$72 (S$100), it said.
The airline, which lists prominent Filipino businessmen on its board of directors, currently flies from Manila to 19 domestic destinations in the Philippines.
Apart from the premium airlines, the Singapore-Manila route is served by budget carriers such as Singapore-based Tiger Airways and Jetstar Asia as well as Cebu Pacific of the Philippines