The 34-year-old said he had not recovered from the injury he suffered at the Miami Masters in March where he finished runner-up to Roger Federer.
"Unfortunately, I have to withdraw from Roland Garros this year," Isner, who has made the last-16 in Paris on three occasions, wrote on Twitter.
"The foot injury I sustained in Miami had not fully healed and there's just no way I could possibly compete on the clay in Paris.
"This is a bump in the road and I'm certain I will fully recover. Hope to see everyone at Wimbledon."
World No 8 Kevin Anderson announced last month that he would also miss the French Open due to an elbow injury.
Roland Garros gets underway in Paris on May 26.