Reports on Wednesday suggested the 44-year-old had suffered a relapse, after having a dangerous growth removed from his salivary gland in November last year.
And the Catalan club have confirmed that Vilanova will be taking a hiatus from the game while he undergoes chemotherapy and radiation treatment that is scheduled to last around six weeks.
“In the process of monitoring the parotid gland, there has been an extension of his condition that will require surgery," read a club statement.
The coach will undergo the surgery on Thursday and is expected to be hospitalised for three to four days.
Vilanova has made an excellent start to his career as Barca coach after taking them to the top of La Liga and dropping just two points from their first 16 games.