| CEB–MNL | Cebu City/Lapu-Lapu City – Manila (Pasay) | 1,090 |
| DVO–MNL | Davao – Manila (Pasay) | 742 |
| HKG–MNL | Hong Kong – Manila (Pasay) | 630 |
| MNL–SIN | Manila (Pasay) – Singapore | 528 |
| ICN–MNL | Seoul – Manila (Pasay) | 528 |
| 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–TPE | Manila (Pasay) – Taoyuan | 433 |
| MNL–MPH | Manila (Pasay) – Caticlan | 413 |
| KUL–MNL | Sepang – Manila (Pasay) | 338 |
| BKK–MNL | Bangkok – Manila (Pasay) | 321 |
| CEB–DVO | Cebu City/Lapu-Lapu City – Davao | 299 |
| DXB–MNL | Dubai – Manila (Pasay) | 280 |
| DGT–MNL | Dumaguete City – Manila (Pasay) | 259 |
| MNL–TAG | Manila (Pasay) – Panglao | 253 |
| MNL–NRT | Manila (Pasay) – Narita | 248 |
| 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 |
| MNL–SGN | Manila (Pasay) – Ho Chi Minh City | 195 |
| HAN–MNL | Hanoi (Soc Son) – Manila (Pasay) | 187 |
| MNL–RUH | Manila (Pasay) – Riyadh | 167 |
| CAN–MNL | Guangzhou (Huadu) – Manila (Pasay) | 163 |
| CEB–NRT | Cebu City/Lapu-Lapu City – Narita | 155 |
| DAD–MNL | Da Nang – Manila (Pasay) | 150 |
| MNL–SYD | Manila (Pasay) – Sydney (Mascot) | 144 |
| CEB–ICN | Cebu City/Lapu-Lapu City – Seoul | 143 |
| KIX–MNL | Osaka – Manila (Pasay) | 142 |
| MNL–PVG | Manila (Pasay) – Shanghai (Pudong) | 138 |
| KLO–MNL | Kalibo – Manila (Pasay) | 130 |
| CEB–CGY | Cebu City/Lapu-Lapu City – Laguindingan | 125 |
| BXU–CEB | Butuan – Cebu City/Lapu-Lapu City | 115 |
| DPS–MNL | Kuta, Badung – Manila (Pasay) | 111 |
| MNL–OZC | Manila (Pasay) – Ozamiz | 105 |
| CEB–SIN | Cebu City/Lapu-Lapu City – Singapore | 101 |
| CEB–ILO | Cebu City/Lapu-Lapu City – Cabatuan | 96 |
| CRK–HKG | Mabalacat – Hong Kong | 92 |
| CEB–HKG | Cebu City/Lapu-Lapu City – Hong Kong | 91 |
| DPL–MNL | Dipolog – Manila (Pasay) | 87 |
| KHH–MNL | Kaohsiung (Xiaogang) – Manila (Pasay) | 81 |
| MNL–TUG | Manila (Pasay) – Tuguegarao City | 81 |
| MFM–MNL | Nossa Senhora do Carmo – Manila (Pasay) | 80 |
| MNL–PAG | Manila (Pasay) – Pagadian | 79 |
| MEL–MNL | Melbourne – Manila (Pasay) | 77 |
| MNL–NGO | Manila (Pasay) – Tokoname | 74 |
| FUK–MNL | Fukuoka – Manila (Pasay) | 72 |
| CGK–MNL | Jakarta – Manila (Pasay) | 71 |
| MNL–RXS | Manila (Pasay) – Roxas City | 67 |
| LAO–MNL | Laoag City – Manila (Pasay) | 60 |
| DMK–MNL | Bangkok – Manila (Pasay) | 60 |
| CEB–CRK | Cebu City/Lapu-Lapu City – Mabalacat | 55 |
| CEB–MPH | Cebu City/Lapu-Lapu City – Caticlan | 49 |
| CEB–PAG | Cebu City/Lapu-Lapu City – Pagadian | 48 |
| BWN–MNL | Bandar Seri Begawan – Manila (Pasay) | 48 |
| DVO–ILO | Davao – Cabatuan | 48 |
| CRK–SIN | Mabalacat – Singapore | 47 |
| 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 |
| CRK–MPH | Mabalacat – Caticlan | 42 |
| CYZ–MNL | Cauayan City – Manila (Pasay) | 42 |
| CEB–KIX | Cebu City/Lapu-Lapu City – Osaka | 39 |
| BKK–CRK | Bangkok – Mabalacat | 39 |
| MNL–VRC | Manila (Pasay) – Virac | 32 |
| CRK–NRT | Mabalacat – Narita | 29 |
| CRK–DVO | Mabalacat – Davao | 28 |
| CEB–DMK | Cebu City/Lapu-Lapu City – Bangkok | 22 |
| GES–ILO | General Santos – Cabatuan | 22 |
| DVO–ZAM | Davao – Zamboanga | 18 |
| BCD–DVO | Bacolod City – Davao | 16 |
| DVO–PPS | Davao – Puerto Princesa | 13 |
| CRK–ILO | Mabalacat – Cabatuan | 10 |
| DVO–MPH | Davao – Caticlan | 9 |
| ILO–PPS | Cabatuan – Puerto Princesa | 8 |
| DVO–TAC | Davao – Tacloban City | 7 |
| HKG–ILO | Hong Kong – Cabatuan | 6 |
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