The attacker, only described as wearing a black shirt and blue pants, was the subject of a broad search Sunday by the sheriff's departments of Calaveras and surrounding counties, the California Highway Patrol and the state Department of Justice.
Eight-year-old Leila Fowler was stabbed to death on Saturday at the home in Valley Springs, Coroner Kevin Raggio said. The town has about 2,500 people.
"This is way too close to home," Julia Poland, who took her 13-year-old daughter to an afternoon news conference on the search, told the Modesto Bee. "This kind of thing does not happen here."
Leila was found by her brother - reported by local media to be 12-years-old - after he encountered a male intruder in the home. When the intruder ran away, the boy found his sister stabbed. She was pronounced dead at a local hospital, officials said.
Authorities spent Saturday night and into Sunday conducting a door-to-door sweep of homes scattered across hilly terrain, checking storage sheds and horse stables, and even searching attics.
"It is a difficult area to search, it's rural, remote," sheriff's Capt. Jim Macedo said.
Mass notifications alerted residents about the incident and the search for the suspect, officials said.
"I was working on my tractor and a CHP copter kept flying over my house," area resident Roger Ballew, 35, told The Associated Press on Sunday.
A SWAT team showed up at his house Saturday night and told him to stay inside, Ballew said.
"It was nerve-wracking, I didn't sleep well," he said.
Investigators on Sunday were interviewing several people, but no suspects had been named by late afternoon. Investigators were checking out tips that had come in to the sheriff's office, including leads and tips that came from outside the county, officials said.
"It's just terrible," area resident Paul Gschweng told Sacramento television station KCRA. "What can I say about it, it's just a tragedy."
The station reported that a neighbor told police that a man was running from the girl's home after the incident.
Investigators were asking area residents to call authorities if they had any information, or knew of anyone who may have unexplained injuries, or may have left the area unexpectedly after the girl was killed.
Valley Springs is a community of about 2,500 people in an unincorporated area of Calaveras County, known as "Gold Country," in the foothills of the Sierra Nevada mountains, about 60 miles southeast of Sacramento.
The county became world-famous in 1865 with Mark Twain's short story, "The Celebrated Jumping Frog of Calaveras County," according to the Calaveras County Chamber of Commerce website.