Mokry currently the deputy chairman beat former Czech Republic international Ivan Hasek in a secret ballot at the federation's general meeting in Prague the soccer body said in a statement.
Mokry replaces Jan Obst for a four-year-term. He faces a difficult task to restore confidence in soccer damaged by a scandal that broke last May when police wiretappings revealed attempts to fix matches.
Since then more than two dozen soccer officials and referees have been suspended or fined for offering or accepting bribes and are awaiting trial.
A soccer referee received an eight-month suspended sentence last month for agreeing to accept a bribe to fix a game last year.
In November Milan Brabec - another federation vice chairman - was suspended and fined in connection with the bribery scandal.
Five Czech teams of the two top leagues had points deducted at the end of the season for their involvement in the scandal.