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After 58 days of running, she was met by proud family members as she crossed the Te Araroa Trail finish line, in Bluff, at 10pm yesterday.
It meant Ms Thomas smashed the previous record — set by Australian Lucy Clark — by a week.
But that was not what the 3000km journey was about, she said.
"To be completely honest, the record is awesome and I’m really stoked about it, but it was way more about the adventure for me.
"Every day has been epic.
"It’s been so hard, so rewarding, and so challenging."
Ms Thomas had wanted to run the trail since getting a pacemaker a decade ago, and set off from Cape Reinga on November 26.
"That is what I have wanted to do with this run — inspire any kids, whether they have got a heart condition, a health condition or even just a kid in general, to get out there, do whatever makes them happy, and keep pushing their own boundaries."
Along the way, she raised about $21,000 for the HeartKids NZ charity to give back for the support and medical expertise she had received.
Heart Kids chief executive Mark Longbottom said the team were in awe of Ms Thomas’ achievement.
“[We] are so impressed by Brooke ... Her fundraising efforts will go a long way to help support Kiwi children living with congenital heart conditions."
Ms Thomas credited her running coach, ultra-runner Adam Keen, of AerobicEdge, and her family for her success.
"You are only had strong as your support group."