Patton has a condition called 'jumper's knee', and will visit a specialist in Stockholm in January.
He is expected to resume full training in April but will not be considered for selection until at least a month later.
"It is not an uncommon condition in young players and something the club was aware of before we drafted Jonathon," Giants sports science manager John Quinn said on Tuesday.
"As such, he has been on a modified training program since he joined the Giants and we have been monitoring him closely."
Stephen Coniglio, picked immediately after Patton in the NAB AFL Draft, saw the same specialist in Stockholm, Sweden, earlier this year and responded positively.
"We need to take a very cautious approach with Jonathon and do whatever is required to get his knee right," Quinn said.
"The club is aware that there are expectations of all draftees, particularly the number one pick, but we also believe Jonathon will be a 10-year player for the Giants and we want to give him every chance to achieve full fitness and fulfil his potential at the highest level."
