Choi had nine top-10 finishes in her rookie season, but was surpassed by Yani Tseng for rookie-of-the-year honors.
She fired a 3-under 68 over the Saucon Valley Country Club course to take a one-shot advantage over 2007 champion Cristie Kerr, qualifier Jean Reynolds and world No. 1 Lorena Ochoa. The only other player under par was Hee Young Park, who shot a 70.
Ochoa climbed to the top spot in the world rankings thanks to 21 victories over a span of three years beginning in 2005. She has added two triumphs this season in eight events.
She highlighted her round with a 50-foot birdie putt at the par-3 11th, her second hole of the day.
"I think I made longer putts before, but this is the one with more breaks," Ochoa said. "It first went left and went right, went left and went left and then went right. I didn't know what it was. It was like a good surprise.
"Anything in the red numbers to start a U.S. Open, I will always take it."
Choi reached 5-under through 12 holes before faltering late in her round.
Those at 71, tied for sixth place, included LPGA Championship winner Anna Nordqvist, Candie Kung, Eun Hee Ji, Kristy McPherson, Young Kim and amateur Alexis Thompson.
Thompson became the youngest player ever to compete in the U.S. Women's Open when she played in the tournament two years ago at age 12.