The franchise had signed Brown through until 2022 but that was dependent on his international commitments.
With Brown linked to the main coaching candidates for the vacant All Black position, there was a fear he would coach for the 2020 season only and then move on.
However, with Brown joining Brave Blossoms head coach Jamie Joseph in Japan through until the next World Cup, he is now able to coach the Highlanders for the next three seasons.
Highlanders chief executive Roger Clark is thrilled Brown has confirmed he will stay until 2022 with the Highlanders.
"It is a massive coup for us. Everybody wants him - the All Blacks wanted him and now we have got him for the next three years," Clark said.
"It's incredibly exciting for our fans."
Clark said it was a real boost for the young players in the team to have Brown involved on the attack side.
Brown, who will be the attack coach and also be in charge of the game plan, would have a significant workload through the year but, with the way Super Rugby was structured, it should be manageable, Clark said.
The Super Rugby season will start early next year - the first round is in late January and it will be over by June.
The test windows are in July and November, when the Highlanders are not playing.
From 2021, the Super Rugby competition will go from mid to late February to the end of June when it reverts to a true round-robin format.
Clark said Brown had been doing two jobs for a good while so he was used to it and was a good manager of time.
Brown was also an assistant coach and not the head coach, so that would make his job easier.