Freund, the winner of the last World Cup in Oslo before the trip to the Czech Republic, didn't produce the best points total from either round but he was the most consistent.
Having won three World Cups since last month's Winter Olympics and been on the podium twice more, Freund leapt 203.5m and 191.5m for the second best total of each round.
That gave him an overall total of 391.0 with two rounds to come with Norwegian Anders Bardal second with 379.9 and Peter Prevc third with 375.6 in Harrachov.
Noriaki Kasai could break into the top three at 41-years-old as he is just a point behind Prevc while World Cup champion elect Kamil Stoch is fifth with a total of 363.8.
If Freund maintains his lead after the third and fourth jumps he will become the first German to win the ski flying world title since Sven Hannawald defended his crown in 2002.
- Sports & Recreation
- Peter Prevc