The 23-year-old, who underwent successful surgery on his right Achilles in London early last year, will undergo a similar operation on his left Achilles next week.
This time the surgery will take place in Geelong.
"He's got a little anomaly … down in his Achilles," club physio Mike Snelling told CatsTV.
"There's a little muscle and tendon called plantaris, and that has sort of … grown into his Achilles.
"He'll have that excised in surgery next week."
Cowan's recovery from the operation is expected to take around 12 weeks.
"All things going well, he should be up and running for the beginning of pre-season," Snelling said.
"Hopefully we then see him for a full year next year."
AFL.com.au understands that Cowan has been told that he will remain with the Cats next season.
But no decision has been made about whether the speedy onballer stays on the senior list or is redrafted as a rookie.
Recruited from Daylesford via the North Ballarat Rebels, Cowan made his AFL debut in 2011.
He played three games at the highest level that season but is yet to play another one.
