| 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 |
| DOH–MNL | Doha – Manila (Pasay) | 221 |
| 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 |
| HND–MNL | Tokyo – Manila (Pasay) | 187 |
| MNL–RUH | Manila (Pasay) – Riyadh | 167 |
| CEB–NRT | Cebu City/Lapu-Lapu City – Narita | 155 |
| DAD–MNL | Da Nang – Manila (Pasay) | 150 |
| CEB–IAO | Cebu City/Lapu-Lapu City – Del Carmen | 146 |
| MNL–SYD | Manila (Pasay) – Sydney (Mascot) | 144 |
| KIX–MNL | Osaka – Manila (Pasay) | 142 |
| MNL–PVG | Manila (Pasay) – Shanghai (Pudong) | 138 |
| MNL–SFO | Manila (Pasay) – San Francisco | 135 |
| MNL–XMN | Manila (Pasay) – Xiamen | 125 |
| CEB–CGY | Cebu City/Lapu-Lapu City – Laguindingan | 125 |
| LAX–MNL | Los Angeles – Manila (Pasay) | 117 |
| BXU–CEB | Butuan – Cebu City/Lapu-Lapu City | 115 |
| DPS–MNL | Kuta, Badung – Manila (Pasay) | 111 |
| MNL–OZC | Manila (Pasay) – Ozamiz | 105 |
| CRK–USU | Mabalacat – Coron | 102 |
| CEB–ILO | Cebu City/Lapu-Lapu City – Cabatuan | 96 |
| BNE–MNL | Brisbane – Manila (Pasay) | 95 |
| 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–PEK | Manila (Pasay) – Beijing | 79 |
| MEL–MNL | Melbourne – Manila (Pasay) | 77 |
| MNL–NGO | Manila (Pasay) – Tokoname | 74 |
| FUK–MNL | Fukuoka – Manila (Pasay) | 72 |
| GUM–MNL | Hagåtña – Manila (Pasay) | 72 |
| MNL–YVR | Manila (Pasay) – Vancouver | 71 |
| CGK–MNL | Jakarta – Manila (Pasay) | 71 |
| MNL–RXS | Manila (Pasay) – Roxas City | 67 |
| JJN–MNL | Quanzhou – Manila (Pasay) | 65 |
| LAO–MNL | Laoag City – Manila (Pasay) | 60 |
| DVO–TAG | Davao – Panglao | 57 |
| MNL–PUS | Manila (Pasay) – Busan | 53 |
| CEB–MPH | Cebu City/Lapu-Lapu City – Caticlan | 49 |
| MNL–PER | Manila (Pasay) – Perth | 49 |
| MNL–POM | Manila (Pasay) – Port Moresby | 48 |
| 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 |
| CEB–KIX | Cebu City/Lapu-Lapu City – Osaka | 39 |
| MNL–SEA | Manila (Pasay) – Seattle | 38 |
| MNL–YYZ | Manila (Pasay) – Toronto | 35 |
| JFK–MNL | New York – Manila (Pasay) | 32 |
| ANC–YVR | Anchorage – Vancouver | 32 |
| HNL–MNL | Honolulu, Oahu – Manila (Pasay) | 31 |
| KTI–MNL | Phnom Penh (Boeng Khyang) – Manila (Pasay) | 27 |
| MNL–ROR | Manila (Pasay) – Babelthuap Island | 24 |
| CEB–CRM | Cebu City/Lapu-Lapu City – Catarman | 15 |
| CBO–TWT | Datu Odin Sinsuat – Bongao | 7 |
| CBO–CEB | Datu Odin Sinsuat – Cebu City/Lapu-Lapu City | 6 |
| BPA–CEB | BPA – Cebu City/Lapu-Lapu City | 6 |
| TWT–ZAM | Bongao – Zamboanga | 4 |
| ANC–MNL | Anchorage – Manila (Pasay) | 2 |
| CEB–NGOonce | Cebu City/Lapu-Lapu City – Tokoname | 1 |
.jpg){kind=link}