Portuguese Morais, 29, sustained the injury during training on Monday and will be sidelined for up to nine months.
The club said on its official Twitter account: “Following the results of Filipe Morais’ scan, the club can confirm that the Portuguese winger has ruptured his anterior cruciate ligament.
“Morais is set to be sidelined now for anything between six to nine months due to the injury, meaning he could sadly miss the whole season.”
Bradford boss Phil Parkinson revealed Morais’ injury after his side’s 2-1 friendly defeat at Guiseley on Tuesday night.
“It is a big blow for us,” Parkinson said. “It was a low day down at the training ground given that one of our key players had just got injured.”
Morais, who progressed through Chelsea’s academy, joined Bradford in the summer of 2014 and made a total of 40 appearances last season, scoring six goals.