The former Celta Vigo coach took over at Camp Nou last month following the departure of Gerardo Martino.
A statement on the club's official website confirmed the news of his procedure.
"FC Barcelona's coach, Luis Enrique Martinez, has had an emergency operation for acute appendicitis," it read.
"The surgery was successful and he will be discharged in the next day or so."
The 44-year-old spent eight years as a player at Barca after moving from arch-rivals Real Madrid in 1996, winning two La Liga titles, two Copa del Rey crowns and the UEFA Super Cup during his time at the club.
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