The 30-year-old Denmark international had asked to be substituted late in Barcelona's 2-1 win over Getafe last month due to left knee pain and missed his country's subsequent international fixtures.
Braithwaite had initially tried a conservative approach to manage the injury but Barca have confirmed he will go under the knife to resolve the issue.
"Martin Braithwaite has a femoropatellar injury in his left knee which has not responded to conservative treatment," the club wrote in a statement.
"The Danish striker will undergo surgery in the coming days. The club will publish a new injury update when the process has taken place."
It has been widely reported that Braithwaite will not return this calendar year, which is a setback for the Catalans who had forwards Lionel Messi and Antoine Griezmann depart during the recent transfer window.
Braithwaite scored seven goals in 42 appearances in all competitions for the Blaugrana last season, before netting a double in their opening LaLiga win over Real Sociedad.