AirHint found the following cheapest return flights from Heraklion (HER) to Prague (PRG) in September 2025 (see full year).

Return flights

10 Sep - 16 Sep	Smart Wings
10 Sep - 14 Sep	Smart Wings
22 Sep - 27 Sep	SKY express
05 Sep - 12 Sep	SKY express
27 Sep - 30 Sep	SKY express
10 Sep - 20 Sep	SKY express
10 Sep - 27 Sep	SKY express
05 Sep - 20 Sep	SKY express
05 Sep - 08 Sep	SKY express
06 Sep - 12 Sep	Eurowings
28 Sep - 01 Oct	Aegean Airlines
29 Sep - 17 Oct	SKY express
29 Sep - 13 Oct	SKY express
29 Sep - 06 Oct	SKY express
29 Sep - 03 Oct	SKY express
29 Sep - 15 Oct	SKY express
29 Sep - 08 Oct	SKY express
29 Sep - 10 Oct	SKY express
27 Sep - 17 Oct	SKY express
27 Sep - 13 Oct	SKY express

Also check the deals for one-way flights from Heraklion to Prague in September.

The deals are updated regularly. The prices may go up as tickets are purchased by other travellers. Only the cheapest flights are offered. Select a price to book and secure these cheap prices.

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Cheapest return flights from Heraklion to Prague in September from 151€

Return flights