The Visma-Lease a Bike rider took her second national title on the roads of North Yorkshire, beating Claire Steels (Movistar) by 33 seconds. Elinor Barker (Uno-X Mobility) came third, 1:02 behind Henderson.
The winner was almost 40 seconds ahead of Steels at the 15km checkpoint, and increased her lead by the finish on the 30km course.
Interestingly, it was the first victory taken by a rider wearing the Giro Aerohead 2.0, which was launched with much fanfare earlier this year at Tirreno-Adriatico.
Earlier in the day, Josie Nelson (dsm-firmenich PostNL) won the first British national title of the week, in the under-23 women's time trial.
The 22-year-old beat second-placed Maddie Leech of Lifeplus Wahoo by 1:54, with Flora Perkins (Fenix-Deceuninck) a further 18 seconds behind.
The circuit was the same for both the under-23 riders and elites, with two laps of a 15km course, meaning 512m of elevation - it was not a rouleur's favourite.
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With last year's elite women's champion, Lizzie Holden, missing from the start list, there was due to be a new woman in the red, white and blue bands.
A solid time was set early on by Lucy Lee (DAS-Hutchinson-Brother UK), who finished in 50:26.3, which saw her take over the hot seat.
Steels took over the lead late on, setting the fastest split time of 23:14.82, and followed this up with a finishing time of 46:39.9.
However, Henderson was hot on her heels, going faster than Steels at the intermediate check by almost 40 seconds, and finished in 46:07.0 at an average speed of 39.03 km/h.
It was a reminder of her time trialling prowess, which saw her finish fourth at the World Championships last summer, and second at the European Championships in the same event. She is a favourite to medal at the Paris Olympics.
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Earlier on Wednesday, Josie Nelson dominated the under-23 event, setting 24:01.48 at the halfway mark and finishing with a time of 47:58.97. Raced at 37.5km/h, her time would have meant fifth in the elite women's race, proving how impressive her ride was.
Last off was Maddie Leech, the defending champion, who was just 31 seconds down at the halfway mark, but conceded more time on the second lap, eventually finishing in 49:52.5.
Results
British National Road Championships: Women's elite time trial (30km)
1. Anna Henderson, Visma-Lease a Bike, in 46:07
2. Claire Steels, Movistar, +33s
3. Elinor Barker, Uno-X Mobility, +1:02
4. Pfeiffer Georgi, dsm-firmenich PostNL, +1:35
5. Elynor Bäckstedt, Lidl-Trek, +2:07
6. Anna Morris, +2:50
7. Hayley Simmonds, Doltcini O'Shea, +3:21
8. Lucy Lee, DAS-Hutchinson-Brother UK, +4:19
9. Sarah Storey, +4:30
10. Alice Wood, Human Powered Health, +4:36
British National Road Championships: under-23 women's time trial (30km)
