| CEB–MNL | Cebu City/Lapu-Lapu City – Manila (Pasay) | 1,090 |
| DVO–MNL | Davao – Manila (Pasay) | 742 |
| CGY–MNL | Laguindingan – Manila (Pasay) | 514 |
| ILO–MNL | Cabatuan – Manila (Pasay) | 463 |
| MNL–TAC | Manila (Pasay) – Tacloban City | 451 |
| BCD–MNL | Bacolod City – Manila (Pasay) | 447 |
| MNL–MPH | Manila (Pasay) – Caticlan | 413 |
| CEB–DVO | Cebu City/Lapu-Lapu City – Davao | 299 |
| DGT–MNL | Dumaguete City – Manila (Pasay) | 259 |
| MNL–TAG | Manila (Pasay) – Panglao | 253 |
| BXU–MNL | Butuan – Manila (Pasay) | 228 |
| DRP–MNL | Legazpi – Manila (Pasay) | 224 |
| MNL–ZAM | Manila (Pasay) – Zamboanga | 222 |
| MNL–PPS | Manila (Pasay) – Puerto Princesa | 219 |
| GES–MNL | General Santos – Manila (Pasay) | 203 |
| CEB–IAO | Cebu City/Lapu-Lapu City – Del Carmen | 146 |
| CEB–CGY | Cebu City/Lapu-Lapu City – Laguindingan | 125 |
| BXU–CEB | Butuan – Cebu City/Lapu-Lapu City | 115 |
| MNL–OZC | Manila (Pasay) – Ozamiz | 105 |
| CRK–USU | Mabalacat – Coron | 102 |
| CEB–ILO | Cebu City/Lapu-Lapu City – Cabatuan | 96 |
| CEB–USU | Cebu City/Lapu-Lapu City – Coron | 92 |
| DPL–MNL | Dipolog – Manila (Pasay) | 87 |
| CEB–TAC | Cebu City/Lapu-Lapu City – Tacloban City | 86 |
| BCD–CEB | Bacolod City – Cebu City/Lapu-Lapu City | 81 |
| MNL–TUG | Manila (Pasay) – Tuguegarao City | 81 |
| CBO–MNL | Datu Odin Sinsuat – Manila (Pasay) | 80 |
| MNL–RXS | Manila (Pasay) – Roxas City | 67 |
| LAO–MNL | Laoag City – Manila (Pasay) | 60 |
| DVO–TAG | Davao – Panglao | 57 |
| CEB–MPH | Cebu City/Lapu-Lapu City – Caticlan | 49 |
| CEB–ZAM | Cebu City/Lapu-Lapu City – Zamboanga | 47 |
| CEB–GES | Cebu City/Lapu-Lapu City – General Santos | 46 |
| CEB–PPS | Cebu City/Lapu-Lapu City – Puerto Princesa | 43 |
| BSO–CRK | Basco – Mabalacat | 43 |
| CYZ–MNL | Cauayan City – Manila (Pasay) | 42 |
| KTI–MNL | Phnom Penh (Boeng Khyang) – Manila (Pasay) | 27 |
| CEB–CRM | Cebu City/Lapu-Lapu City – Catarman | 15 |
| BPA–CEB | BPA – Cebu City/Lapu-Lapu City | 6 |