Cheapest flight to Prague from Germany is from Bremen.
You can find one way ticket for as low as 22EUR with Ryanair.
Ryanir operates every Tuesday, Thursday and Saturday.
Thu 3 Sep 12:35 Bremen (BRE)
Thu 3 Sep 13:50 Prague (PRG)
Thu 10 Sep 12:35 Bremen (BRE)
Thu 10 Sep 13:50 Prague (PRG)
Thu 17 Sep 12:35 Bremen (BRE)
Thu 17 Sep 13:50 Prague (PRG)
Thu 24 Sep 12:35 Bremen (BRE)
Thu 24 Sep 13:50 Prague (PRG)
In September, you can also get a good deal with Germanwings from Bonn.
For 49EUR, you can flight to Prague at Sunday from Cologne Bonn Airport at 19:50, flight takes 1h 10minutes.
Sun 20 Sep 19:50 Bonn (CGN)
Sun 20 Sep 21:00 Prague (PRG)
For a few EUR more – 53, you can take bit longer route from Bonn to Prague through London, you will have to wait in London for a few hours, bud you can save bit of money that way
Tue 8 Sep 22:10 Bonn (CGN) with Ryanair
Tue 8 Sep 22:40 London (STN)
Wed 9 Sep 6:45 London (STN) with Ryanair
Wed 9 Sep 9:40 Prague (PRG)
For 56 EUR and with one stop also in London, you can travel to Prague from EuroAirport Basel Mulhouse Freiburg
Wed 16 Sep 10:15 Freiburg (BSL) with Ryanair
Wed 16 Sep 10:55 London (STN)
Wed 16 Sep 19:35 London (STN) with Ryanair
Wed 16 Sep 22:30 Prague (PRG)