Henderson started on the third row but moved up to the top-15 by the end of the start loop. She fell back slightly on the first lap, but moved up steadily and was in the top-10 by the halfway point in the race, finishing two minutes and 29 seconds behind winner Annika Langvad (Specialized), the reigning world champion.
"I'm really pleased," Henderson said after the race. "It's the first big race of the season, so you never know quite what to expect and how everyone is going."
"It's a relief to have the first World Cup done. I'm always anxious at the start of the season to see where I will fit in, what I need to work on and what my strengths are.
"I was wearing my pain face for most of the race today. I had a good start but immediately my chest seized up, my hands were cold and I was as stiff as anything. The cold temperature made me feel like I was breathing in icicles.
"It didn’t take too long to find my rhythm though and I felt strong on the steep Czech climbs! Really happy with how I rode today and a sign that the result can certainly be better if and when all comes together on the day.
"Thanks to my small but awesome support crew over here and for all the support from home. Front row next week.
Linda Indergand (Focus XC) took the lead through the start loop, but then Langvad accelerated by her as the race hit the climbs on the first lap.
"Yes, I attacked early," Langvad said, "but I was really not sure I could keep it. I just felt so good, so I thought 'OK, if I feel good now I might as well make it difficult for everyone else and just ride my own pace'."
Rio bronze medalist Catharine Pendrel (Clif Bar) moved into second and, while not catching Langvad, was dropping the rest of the chasers. However, the Canadian dropped her chain through the final rock garden of the lap and then flatted on a descent as she tried to chase back, putting her out of contention.
Sabine Spitz (Wiawis Bikes) moved into second with Indergand maintaining a lock on third. Yana Belomoina (CST Sandd American Eagle) briefly challenged Indergand for third with a lap to go, but then dropped back and had to battle Maja Wloszczowska (Kross Racing) for fourth, with Wloszczowska winning the sprint at the finish.
In the under 23 men's race, Norway's Petter Fagerhaug (Norwegian National Team) quickly took control of the race and was only challenged briefly by Latvian Martins Blums (ZZK). Fagerhaug beat Blums by 35 seconds in the end, with Sebastian Carstensen (CST Sandd American Eagle) taking third, a further five seconds back.
Reece Tucknott was the top Australian finisher, in 16th place, with Australian national champion Tasman Nankervis finishing 26th.