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.