The 38-year-old Iceland international, who has played for top sides likes Chelsea and FC Barcelona, 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 on Monday. 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.
It is not yet clear whether Gudjohnsen was injured in Spain, where the club had a pre-season stint, or in India. The team had returned home from Spain in the second week of this month.
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 on Monday.