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

Return flights

17 Sep - 22 Sep	Eurowings
24 Sep - 29 Sep	Eurowings
06 Sep - 10 Sep	SKY express
03 Sep - 07 Sep	SKY express
19 Sep - 27 Sep	SKY express
19 Sep - 29 Sep	SKY express
17 Sep - 27 Sep	SKY express
17 Sep - 29 Sep	SKY express
19 Sep - 10 Oct	SKY express
19 Sep - 06 Oct	SKY express
19 Sep - 03 Oct	SKY express
17 Sep - 06 Oct	SKY express
17 Sep - 03 Oct	SKY express
05 Sep - 07 Sep	Aegean Airlines
01 Sep - 01 Sep	Smart Wings
29 Sep - 10 Oct	SKY express
29 Sep - 06 Oct	SKY express
29 Sep - 03 Oct	SKY express
12 Sep - 03 Oct	SKY express
29 Sep - 18 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.

Book a cheap hotel in Prague

Cheap car rent in Prague

Cheapest return flights from Heraklion to Prague in September from $209

Return flights