Brannigan, who struggled last year after coming back from a serious injury, said the victory showed he was fit and healthy again.
"It is amazing to be feeling how I was a year or so ago. I have put in a huge amount of work to get back. So this makes me so happy."
Blenkinsop was second, just 0.6 seconds behind with Swiss visitor Nick Beer third in 3:04:26.
Defending champion Brook MacDonald (Trek World Racing) could manage only fifth place, ahead of Kawerau's Matt Walker and Christchurch's Cam Cole.
Atkin, 20, had come to Rotorua hoping for a top three effort, even after topping the seeding run.
Favourite Alanna Columb grabbed the hot seat with a 3:51:85 in the third to last run, but Atkin was in a class of her own, winning with the final run in 3:45:83.
Like all the elite riders, she found it a test to cope with the unavoidable race delays.
"I got hungry, thirsty, warmed up, cooled down, warmed up again, cooled down, got bored," Atkin said. "It is part of racing though.
"I am really stoked to win the national elite title. I was going to be thrilled to get in the top three, so to win my first elite national title is unreal."
Rotorua's Keegan Wright impressed as a rider for the future, winning the under-19 title in 3:14:22, which would have placed him mid-pack in the elite competition, with fellow Rotorua rider Robbie Wong-Toi claiming the under-17 honours.
Results
Female, Elite: Sarah Atkin (Lower Hutt) 3:45:83, 1; Alanna Columb (Queenstown) 3:51:85, 2; Harriet Latchem (Queenstown) 3:52:59, 3; Gabby Malloy (Rotorua) 3:58:13, 4; Amanda Monk (Whakatane) 4:09:01, 5.
Senior: Phoebe Coers (Dunedin) 4:27:31, 1.
Under-19: Georgia Petrie (Christchurch) 4:14:28, 1.
Under-17: Shania Rawson (Papamoa) 5:02:30, 1.
Masters: Donna Pickard (Papamoa) 5:28:78, 1.
Male, Elite: George Brannigan (Havelock North, Trek World Racing) 3:01:40, 1; Sam Blenkinsop (Wanganui, Lapierre International) 3:02:00, 2; Nick Beer (Switzerland) 3:04:26, 4; Rupert Chapman (Christchurch) 3:06:50, 4; Brook MacDonald (Hawkes Bay, Trek World Racing) 3:06:51, 5.
Senior: Tyler Brooker (Christchurch) 3:17:17, 1; Aari Barrett (Hamilton) 3:18:58, 2; Harry Chapman (Christchurch) 3:22:83, 3; Brook Mitchell (Christchurch) 3:23:64, 4; Sam Shaw (Rotorua) 3:23.69, 5.
Under-19: Keegan Wright (Rotorua) 3:14:22, 1; Connor Hamilton (Rotorua) 3:16:28, 2; Josh McCombie (Dunedin) 3:17:77, 3; Jack Humphries (Palmerston North) 3:20:30, 4; Peter Bethell (Auckland) 3:20:51, 5.
Under-17: Robbie Wong-Toi (Rotorua) 3:20:46, 1; Mathew Gillan (Queenstown) 3:21:45, 2; Blair McLeod (Rotorua) 3:23:38, 3; Oscar Perks (Nelson) 3:30:22, 4; Jack Hale (Rotorua) 3:31:71, 5
Under-15: Charlie Makea (Napier) 3:47:83, 1; Lachie MacDonald (Lower Hutt) 3:51:30, 2; Tuhoto-Ariki Pene (Rotorua) 3:53:92, 3; Boaz Hebblethwaite (Christchurch) 3:57:46, 4; Wade Strother (Hawkes Bay) 4:01:31, 5.
Masters 1: Adam King (Rotorua) 3:24:76, 1; Michael Evans (Wellington) 3:31:88, 2; Chris Mancey (Queenstown) 3:44:15, 3; Nathan Timoko (Wellington) 3:50:08, 4; Kevin Warner (Hamilton) 3:51:86, 5.
Masters 2: Dave Hunt (Auckland) 4:03:02, 1; Kerry Halse (Auckland) 4:11:68, 2.