The 30-year-old is ranked 25 in the world and is the current Italian No.1.
He moves through to the next round of the tournament after defeating Frenchman Julien Benneteau in five sets on Saturday.
In a press conference, Fognini said he was "very happy" with how he played.
Fognini will have his work cut out for him, going up against the towering Czech who is currently ranked No.19.
If the Italian wins this match, he will reach his second Grand Slam quarter-final from 39 attempts.
Berdych, on the other hand, has reached a quarter-final or better 16 times in his career.
Fognini is the last surviving Italian Singles player in this year’s Australian Open.
He will take on Berdych on Margaret Court Arena at 12:15 pm.