The 38-year-old Serb pulled out of the clay-court event after also withdrawing from the ongoing Miami Open with a right shoulder injury.
Djokovic last competed at Indian Wells earlier this month, where he was beaten by defending champion Jack Draper in the round of 16.
The 24-time Grand Slam winner captured the Monte-Carlo Masters titles in 2013 and 2015.
American world number seven Taylor Fritz also withdrew from the tournament due to injury on Thursday.
The 2026 edition of the Monte-Carlo Masters is scheduled to run from April 5th to 12th, with world number one Carlos Alcaraz set to defend his title.