Skating to "Breakfast in Baghdad", the 17-year-old began with her trademark triple Axel before landing a triple flip-triple toe combination and a triple Lutz to earn 81.18 points, ahead of American Bradie Tennell and South Korean You Young.
"I'm very happy with my jumps but they were not 100% yet and I'll keep working to make them better for the free skating (segment)," Kihira told reporters.
"I still have practise in the next days and I will determine the program content then.
"For now, the quad Salchow is looking good. I'll keep practising it and depending on my condition I'll determine my final content for the free skating."
Canada's Kirsten Moore-Towers and Michael Marinaro took the lead in the Pairs Short Program ahead of Chinese pairs Peng Cheng and Jin Yang, who finished second, and world champions Sui Wenjing and Han Cong.
The Canadians were the last pair to step on to the ice and scored a personal best 76.36 points with a triple twist, throw triple loop and side-by-side triple toe.
"There are a lot of great teams at Four Continents but of course the reigning World Champions are here and they always push us," Moore-Towers said.
"We're really two of their biggest fans... we're really thrilled to watch them and to learn from them. But of course, we're always hoping to win."
In the Rhythm Dance, American's Madison Hubbell and Zachary Donohue beat team mates Madison Chock and Evan Bates by just 0.19 points.