Flynn flew home to Ireland last weekend citing homesickness and a need to be with his terminally ill grandfather.
The club was hopeful he would eventually return to Alberton, but admitted there was a chance he would stay in Ireland.
But speaking to the Irish Independent newspaper, Kildare boss Jason Ryan said Flynn wanted to play Gaelic football and that he planned to study in Ireland.
"He has missed Gaelic football an awful lot; he's looking forward to being involved maybe in the U-21 game and being involved with the seniors over the course of the year," Ryan said.
"He's an incredibly talented kid with a brilliant attitude, so Port Adelaide's loss will be Kildare's gain.
"He's given himself a great opportunity out there, he gave it time and effort and worked hard.
"The right decision for him, he feels at this moment, is to be in Kildare.
"He's a great guy, he'll go back to college and study and get good qualifications and move on from there."
The Power remain hopeful Flynn will return to complete his two-year deal with the club, saying he is a much-liked character.
Port teammate Andrew Moore said the playing group understood why Flynn had decided to return home, but it was hoped he would soon return.
"It's unfortunate he had to go back home; obviously he was a little bit homesick which was fair enough - I think we all probably would have been the same.
"Everyone saw how raw and lively he is out on the track … he's got the pace and he's got some great skills.
"It's sad that he had to go back but it will be good for him to see his family and friends again and then, like I said, he's always welcome back."
