The Californian, who has two European Tour titles on his resume, parred his first nine holes and had three birdies and a bogey coming in to post a two-under-par 70 for a nine-under total of 134.
He was one stroke clear of first-round leader Hank Lebioda, Keith Mitchell, Brandon Wu and Joseph Bramlett.
"Today was really tough," said Kitayama, who played the par-72 Pebble Beach Golf Links, one of three courses in use over the first three rounds along with par-72 Spyglass Hill and the par-71 Monterey Peninsula course.
"Overall, I'm really happy with where I'm at and how I played today."
Of the group sharing second, three played at Monterey Peninsula, where Wu carded a 66, Mitchell posted a 68 and Bramlett carded a 67.
Lebioda, who opened with a 63 at Monterey Peninsula on Thursday, carded an even-par 72 at Pebble Beach.
Lebioda teed off on 10 and had the solo lead at 10-under after birdies at the 10th and second, but he dropped back with a double-bogey at the par-three fifth.
After gusting winds hit the later starters on Thursday, morning rain and more blustery winds pushed up scores on Friday morning.
More rain and wind was forecast for the weekend, and tee times were moved up to try to miss the worst of it.
England's Justin Rose and Ireland's Seamus Power both said the weather reminded them of home.
"It was a bit of a dreary kind of day, kind of English I suppose," said Rose, whose three-under-par round at Spyglass Hill included a hole-in-one at the par-three 15th.
"A special day always when you manage to have a hole-in-one," he said. "I believe it's my 12th.
"Kind of felt like I could have kicked on from that point a little more," added Rose, who had two late bogeys and finished the day tied for 11th, three shots off the lead.
One day, many seasons
Power headlined a group-sharing sixth on seven-under-par after firing an impressive seven-under-par 64 at Monterey Peninsula that included six birdies and an eagle at the par-five 16th.
Power said he played in the rain through the first five or six holes, with blustery winds around the turn before "the last few holes were very pleasant.
"It was one of those days kind of like back home in Ireland where you get a lot of seasons in one day," he said.
"Even when you get opportunities in the fairway the greens because of the rain are soft. So trying to keep the ball close to the hole, it can be challenging. I was able to make some putts to cover up some of the mistakes."
Play was stopped at the 11th hole at Pebble Beach after a caddie for one of the amateur players collapsed and received CPR before being taken to a nearby hospital.
"During the second round of the AT&T Pebble Beach Pro-Am, there was a medical emergency at No. 11 at Pebble Beach involving an amateur's caddie," the PGA Tour said in a statement. "The caddie has been rushed to Montage Health for evaluation."
The PGA Tour players in that group, Max McGreevy and Beau Hossler, were allowed to take some time to collect themselves, warm up and resume play.
Golf Channel reported that the caddie was expected to recover.
