Japan's Sara Takanashi won the gold, having soared a combined 10.5 meters farther than Hendrickson on two jumps off the K95 hill. Takanashi scored 276.5 points when judges' style points were factored in, while Hendrickson scored 265.0.
Germany's Carina Vogt was third at 255.0.
Though the 15-year-old Takanashi jumped 3 1/2 meters longer, she and Hendrickson were tied after their first jump because Hendrickson scored better with her form and landing. On the second jump, though, Takanashi soared 7 meters farther and maintained good enough form to claim the victory.
"Sarah and Sara are the two strongest jumpers on the Earth right now," said Paolo Bernardi, the international coach for Women's Ski Jumping USA. "They are both shooting stars. It was nice to watch a battle to win because it was such a high level of ski jumping."
Hendrickson said she had a hard time getting accustomed to the hill and handle the expectations that her surprising success this season put on her. She has a huge lead in the senior-level World Cup standings, and is likely to win the overall championship next month.
"I'm still a junior and I wanted to really focus to keep my goals set high for junior worlds," she said. "Being in contention for the overall World Cup title means that some people automatically assume I will win every competition. It's not that easy because there are great jumpers here and everyone has the same goal, and I put a lot of pressure on myself this week.
"Sara jumped amazing and definitely had the best jumps on the hill Thursday and deserved the win 100 percent," she added.
Hendrickson will continue the World Cup tour with three competitions March 3-4 in Zao, Japan - one is a make-up for a previous cancellation in Poland - before the World Cup finale March 9 in Oslo, Norway.
"It's not easy to be on top of the world," Bernardi said. "I'm so proud of how she handled the situation and fought back after rough training rounds to get an amazing silver-medal result."