The 38-year-old Iceland international, who has played for top sides likes Chelsea and FC Barcelona, has suffered an injury during a pre-season training.
Club sources said Gudjohnsen, a former Iceland captain with 88 international caps under his belt, is returning home tomorrow. ISL kicks off on October 1 in Guwahati.
"Gudjohnsen is leaving for home tomorrow. He suffered an injury at a pre-season training session," a club source told PTI.
The ace forward did not participate in FC Pune City's practice match against Ozone FC earlier this week.
FC Pune City are on the lookout for a replacement ahead of their ISL's opening fixture against Mumbai City FC on October 3 at Balewadi Sports Complex in Pune.
Club officials are expected to make an official announcement tomorrow.