Lynn has today been announced as the assistant coach for Argentina.
He returned to the Highlanders as a coach this year after spending his late playing and early coaching years with Lyon in France.
“When I returned from France, my intention was always to see out my contract with the Highlanders, but an opportunity to coach at the international level has always been a personal goal of mine," Lynn said in a statement.
"I am delighted to be taking up the role with the Pumas but obviously disappointed I will not be carrying on with the Highlanders. I hugely appreciate everything this organisation has done for me.
"I’ve loved this season and look forward to watching the team in the next few years."
Highlanders chief executive Roger Clark said the club was proud of Lynn.
"We will certainly miss him in our coaching team. However, it’s natural, for both players and coaches, to strive for a national team.
"We wish Kenny, Becs and the kids the very best on their next adventure.”
An announcement about a replacement for Lynn will be made later this year.
