Hanlen cut Henderson's lead back to 30 seconds and, in a thrilling last lap, the New Zealander grabbed the lead.
She said she was happy to win the event especially with the Commonwealth Games coming up this year.
"The [Commonwealth Games] is my big goal but yeah, again, you've got to qualify and you've got to earn it, I believe.
"I've still got to go overseas and prove it but this is a good step for me.
"If I make Com Games selection, I'll go into Europe and give it my all," Hanlen said.
Unfortunately, NZXC member Fluker had two flat tires in the race and finished eighth overall.
Fellow NZXC-rider Katie O'Neill (Rotorua) finished sixth in the race.
Meanwhile, Rotorua's Dirk Peters finished on the podium in the men's elite race, claiming third.
Peters competed against a tough field in the men's cross country race, finishing behind Olympian Dan McConnell (Australia) and Christchurch's Anton Cooper.
Fellow NZXC-rider Carl Jones was not far behind Peters in fourth.
The NZXC Racing team posted on their Facebook page after the event, congratulating their team members.
"In the men's, it was all on from the start with Dan [McConnell] and Anton [Cooper] having a good battle up the front, but Dan was just too fast for everyone and took the win.
"Dirk [Peters] dug deep and left it all out on the track and managed a good 3rd place with Carl [Jones] again not far behind in 4th. Time for a rest and gear up for the team's first World Cup in Cairns."
The Rotorua-based NZXC Racing team also produced another good result at the weekend, with Rotorua's Amber Johnston winning the Oceania under-23 women's race.
The New Zealand Olympic Committee will select their team for the 2014 Glasgow Commonwealth Games later this year.