The 18-time Grand Slam champion, who won the crown at Roland Garros in 2009, has been in strong form this year, taking home titles at Indian Wells and Miami.
The 35-year-old also claimed his fifth Australian Open crown in January when he defeated Rafael Nadal in the final in Melbourne.
However, in order to prolong his career, the Swiss pro has decided that he needs to manage his schedule.
In a statement on his official website, Federer said: "Regrettably, I've decided not to participate in the French Open. I've been working really hard, both on and off the court, during the last month but in order to try and play on the ATP World Tour for many years to come, I feel it's best to skip the clay court season this year and prepare for the grass and hard court seasons.
"The start to the year has been magical for me but I need to recognize that scheduling will be the key to my longevity moving forward. Thus, my team and I concluded today that playing just one event on clay was not in the best interest of my tennis and physical preparation for the remainder of the season.
"I will miss the French fans, who have always been so supportive and I look forward to seeing them at Roland Garros next year."
Federer withdrew from the tournament last year with a back injury.