Canterbury's Sam Blenkinsop, who boasts a world ranking of five, was third, stopping the clock at 3m05.82s.
When asked how he was going to celebrate back-to-back national titles Brannigan replied: "There's not a lot to do in Rotorua on a Sunday night. I think we will just be watching television at a mate's place."
Before his final run Brannigan, who finished 22nd in his last World Cup series, had set the fastest seeding time, with a 3m00.69s run, nearly five seconds better than his closest rival. "I got three (minutes) flat in seeding and didn't pedal too hard, so I knew I could break it, so I just pedalled hard and it worked out.
"Coming down in the final I had a couple of moments, but that's just natural because the track is so loose, so I was like, 'Man I hope I stay on', and I did," Brannigan said.
He pointed out he didn't let the fact he was the defending champion play on his mind or change his tactics.
"To be honest I just treated it like another nationals because in New Zealand everyone is so laid back it doesn't get too serious, and I think that helped because I didn't feel any pressure," Brannigan said.
He will have a couple of days rest at home in Havelock North this week before returning to his Queenstown base to continue training for next month's Crankworx event in Rotorua. Brannigan will be easy to spot there.
He will be the rider wearing a top with the New Zealand flag all the way down his left sleeve - his reward for winning the national title again.
The other Hawke's Bay rider among the major placegetters yesterday was Napier's Charlie Makea, who was fifth in the under-17 boys division with a time of 3m50.64s.
Queenstown's Alanna Columb won the women's elite title with a time of 3m51.38s. This was her maiden title.
The woman who beat her last year, Lower Hutt's Sarah Atkin, was second yesterday in 3m52.45s.