Heraklion International Airport offers nonstop service to 122 destinations, served by 50 airlines.
| Destination | Code | Country | Distance | Duration | Airlines |
|---|---|---|---|---|---|
| Chania | CHQ | Greece | 96 km | 1h 0m | TB |
| Thira | JTR | Greece | 121 km | 0h 40m | A3 |
| Paros | PAS | Greece | 187 km | 0h 50m | A3 |
| Naxos, Cyclades Islands | JNX | Greece | 196 km | 0h 50m | A3 |
| Syros Island | JSY | Greece | 232 km | 1h 0m | A3 |
| Mykonos | JMK | Greece | 233 km | 0h 50m | A3 |
| Kos | KGS | Greece | 236 km | 0h 55m | A3 |
| Rhodes | RHO | Greece | 288 km | 1h 0m | GQ, NO, A3 |
| Athens | ATH | Greece | 308 km | 0h 50m | GQ, A3 |
| Kalamata | KLX | Greece | 342 km | 1h 5m | A3 |
| Mytilene | MJT | Greece | 431 km | 1h 15m | A3 |
| Volos | VOL | Greece | 479 km | 1h 30m | GQ |
| Thessaloniki | SKG | Greece | 607 km | 1h 10m | FR, GQ, A3 |
| Alexandroupolis | AXD | Greece | 616 km | 1h 15m | A3 |
| Kerkyra | CFU | Greece | 663 km | 1h 20m | A3 |
| Istanbul | IST | Turkiye | 727 km | 1h 35m | A3 |
| Larnaca | LCA | Cyprus | 770 km | 1h 25m | A3, CY, GQ |
| Tirana | TIA | Albania | 826 km | 1h 35m | A3, GQ |
| Sofia | SOF | Bulgaria | 830 km | 1h 35m | FB |
| Catania | CTA | Italy | 936 km | 2h 0m | FR |
| Haifa | HFA | Israel | 952 km | 2h 30m | E2 |
| Tel Aviv-Yafo | TLV | Israel | 971 km | 1h 40m | A3, LY, IZ |
| Bari | BRI | Italy | 977 km | 1h 50m | V7 |
| Craiova | CRA | Romania | 1,003 km | 1h 50m | A2 |
| Bucharest | OTP | Romania | 1,028 km | 1h 55m | A2, W4 |
| Palermo | PMO | Italy | 1,122 km | 2h 0m | V7 |
| Belgrade | BEG | Republic of Serbia | 1,131 km | 2h 0m | JU |
| Naples | NAP | Italy | 1,134 km | 2h 5m | V7, U2 |
| Brasov | GHV | Romania | 1,151 km | 2h 5m | A2 |
| Sibiu | SBZ | Romania | 1,164 km | 2h 10m | A2 |
| Timisoara | TSR | Romania | 1,207 km | 2h 0m | A2 |
| Cluj-Napoca | CLJ | Romania | 1,277 km | 2h 5m | W4 |
| Chisinau | RMO | Republic of Moldova | 1,325 km | 2h 20m | U5 |
| Iasi | IAS | Romania | 1,330 km | 2h 10m | A2 |
| Rome | FCO | Italy | 1,332 km | 2h 20m | AZ, NO, W4, A3 |
| Suceava | SCV | Romania | 1,375 km | 2h 20m | A2 |
| Budapest | BUD | Hungary | 1,430 km | 2h 25m | W6 |
| Kosice | KSC | Slovakia | 1,515 km | 2h 25m | QS |
| Graz | GRZ | Austria | 1,528 km | 2h 20m | EW, XR |
| Bologna | BLQ | Italy | 1,561 km | 2h 35m | NO, FR |
| Bratislava | BTS | Slovakia | 1,569 km | 2h 30m | QS |
| Vienna | VIE | Austria | 1,587 km | 2h 30m | OS, FR, XR |
| Verona | VRN | Italy | 1,643 km | 2h 30m | V7, NO |
| Brno | BRQ | Czech Republic | 1,683 km | 2h 45m | QS |
| Krakow | KRK | Poland | 1,694 km | 2h 43m | W6 |
| Ostrava | OSR | Czech Republic | 1,695 km | 2h 35m | QS |
| Linz | LNZ | Austria | 1,695 km | 2h 35m | XR |
| Salzburg | SZG | Austria | 1,711 km | 2h 40m | EW |
| Milan | BGY | Italy | 1,736 km | 2h 45m | NO, FR |
| Milan | LIN | Italy | 1,750 km | 2h 40m | AZ |
| Katowice | KTW | Poland | 1,752 km | 2h 45m | XR |
| Innsbruck | INN | Austria | 1,753 km | 2h 40m | EW |
| Yerevan | EVN | Armenia | 1,772 km | 2h 40m | 3F |
| Milan | MXP | Italy | 1,797 km | 2h 55m | U2, NO, FR, W6, W4 |
| Munich | MUC | Germany | 1,817 km | 2h 50m | A3, DE, LH, X3, 4Y |
| Prague | PRG | Czech Republic | 1,863 km | 2h 55m | QS |
| Memmingen | FMM | Germany | 1,869 km | 3h 5m | MI |
| Friedrichshafen | FDH | Germany | 1,886 km | 3h 10m | MI, EW |
| Warsaw | WAW | Poland | 1,899 km | 2h 50m | W6, XR, LO |
| Zurich | ZRH | Switzerland | 1,926 km | 3h 5m | A3, WK, DE, W2, CS, XR |
| Marseille | MRS | France | 1,933 km | 3h 10m | V7, GQ, TO |
| Nuremberg | NUE | Germany | 1,947 km | 3h 0m | DI, XR |
| Berne | BRN | Switzerland | 1,955 km | 3h 5m | 2L |
| Dresden | DRS | Germany | 1,978 km | 3h 5m | XR |
| Stuttgart | STR | Germany | 1,979 km | 3h 5m | DE, EW, X3 |
| Basel, Switzerland/Mulhouse | BSL | France | 1,997 km | 3h 13m | U2, XR |
| Geneva | GVA | Switzerland | 2,004 km | 3h 10m | LX, U2 |
| Montpellier | MPL | France | 2,034 km | 3h 20m | TO |
| Lyon | LYS | France | 2,047 km | 3h 15m | TO, V7, GQ, U2 |
| Strasbourg | SXB | France | 2,056 km | 3h 15m | V7 |
| Leipzig/Halle | LEJ | Germany | 2,065 km | 3h 10m | DI, XR |
| Berlin | BER | Germany | 2,105 km | 3h 10m | DE, EW, U2, FR, XR |
| Frankfurt | FRA | Germany | 2,116 km | 3h 20m | A3, DE, X3, 4Y, XR |
| Barcelona | BCN | Spain | 2,118 km | 3h 25m | VY |
| Saarbruecken | SCN | Germany | 2,133 km | 3h 25m | MI |
| Vilnius | VNO | Lithuania | 2,145 km | 3h 28m | BT |
| Metz/Nancy | ETZ | France | 2,166 km | 3h 15m | A3 |
| Gdansk | GDN | Poland | 2,179 km | 3h 15m | W6 |
| Luxembourg | LUX | Luxembourg | 2,213 km | 3h 20m | LG |
| Toulouse | TLS | France | 2,234 km | 3h 35m | V7 |
| Paderborn | PAD | Germany | 2,238 km | 3h 25m | MI |
| Cologne | CGN | Germany | 2,254 km | 3h 25m | EW, XR |
| Hanover | HAJ | Germany | 2,262 km | 3h 20m | X3, XR |
| Rostock-Laage | RLG | Germany | 2,296 km | 3h 25m | XR |
| Dusseldorf | DUS | Germany | 2,303 km | 3h 25m | DE, EW, X3, XR |
| Muenster | FMO | Germany | 2,324 km | 3h 30m | XR |
| Hamburg | HAM | Germany | 2,352 km | 3h 30m | DE, EW, DI |
| Bremen | BRE | Germany | 2,352 km | 3h 35m | MI, XR |
| Brussels | CRL | Belgium | 2,368 km | 3h 40m | FR |
| Eindhoven | EIN | Netherlands | 2,387 km | 3h 40m | HV, OR |
| Paris | ORY | France | 2,388 km | 3h 45m | TO |
| Paris | CDG | France | 2,390 km | 3h 45m | A3, U2, AF, GQ |
| Brussels | BRU | Belgium | 2,397 km | 3h 40m | SN, TB, GQ |
| Riga | RIX | Latvia | 2,400 km | 3h 35m | BT |
| Bordeaux | BOD | France | 2,431 km | 3h 50m | U2, V7 |
| Copenhagen | CPH | Denmark | 2,449 km | 3h 40m | D8, SK |
| Lille | LIL | France | 2,453 km | 3h 45m | GQ, V7 |
| Rotterdam | RTM | Netherlands | 2,473 km | 3h 40m | HV |
| Amsterdam | AMS | Netherlands | 2,482 km | 3h 50m | HV, OR |
| Deauville | DOL | France | 2,562 km | 3h 45m | A3 |
| Nantes | NTE | France | 2,580 km | 4h 0m | TO, U2, GQ, V7 |
| Tallinn | TLL | Estonia | 2,677 km | 4h 5m | BT |
| London | LGW | United Kingdom | 2,682 km | 4h 10m | BA, U2, XR, LS |
| London | STN | United Kingdom | 2,700 km | 4h 10m | LS |
| London | LHR | United Kingdom | 2,717 km | 4h 5m | BA |
| London | LTN | United Kingdom | 2,736 km | 4h 10m | U2, LS |
| Stockholm | ARN | Sweden | 2,753 km | 3h 55m | SK |
| Bournemouth | BOH | United Kingdom | 2,763 km | 4h 10m | LS |
| Helsinki | HEL | Finland | 2,777 km | 3h 55m | AY |
| Brest | BES | France | 2,828 km | 4h 20m | V7 |
| Leicestershire | EMA | United Kingdom | 2,847 km | 4h 25m | LS |
| Birmingham | BHX | United Kingdom | 2,849 km | 4h 25m | LS, U2 |
| Bristol | BRS | United Kingdom | 2,849 km | 4h 15m | U2, LS |
| Leeds | LBA | United Kingdom | 2,929 km | 4h 30m | LS |
| Manchester | MAN | United Kingdom | 2,933 km | 4h 30m | LS, U2, XR |
| Oslo | OSL | Norway | 2,943 km | 4h 10m | DY |
| Liverpool | LPL | United Kingdom | 2,964 km | 4h 25m | U2, LS |
| Newcastle | NCL | United Kingdom | 3,006 km | 4h 33m | LS |
| Edinburgh | EDI | United Kingdom | 3,150 km | 4h 40m | LS, U2 |
| Dublin | DUB | Ireland | 3,166 km | 4h 45m | EI |
| Glasgow | GLA | United Kingdom | 3,200 km | 4h 45m | LS |
| Belfast | BFS | United Kingdom | 3,229 km | 4h 45m | LS |