In an interview with Sacramento television station KOVR on Friday, Priscilla Rodriquez said her son "could never hurt his sister."
The boy who has not been named by authorities was arrested Saturday. He will be charged with homicide, Calaveras County Sheriff Gary Kuntz said.
In the interview, Rodriquez said, "I know my son could never hurt his sister.
"They never used to fight when they were little," she said.
Rodriquez told the station that a bitter custody battle had driven a wedge between her and the children's father.
The April 27 attack on Leila Fowler shook the tightknit Valley Springs community of about 7,400 people and set off a massive manhunt.
Investigators did a door-to-door sweep of homes, storage sheds and horse stables scattered across the oak-studded hills foothills of the Sierra Nevada. Divers also searched two nearby reservoirs in search of clues.
After hearing Leila's brother had been arrested, residents were in disbelief.
"I did not want to believe it. You kind of thought so, but it's not something you want to believe," Tammy Ainsworth told Sacramento's KCRA-TV.
By Sunday, investigators had released few details of the arrest and did not return calls from The Associated Press seeking details of what led them to arrest the boy.
The boy had told police he found his sister's body and encountered an intruder in the home while their father and stepmother were at a Little League game. He described the man as being tall with long gray hair. But afterward, police said there was no sign of a burglary or robbery.
A neighbor told detectives she saw a man flee the home, but she later recanted the story and was discredited by police.
As part of the investigation, authorities seized several knives from the Fowler home, where Leila lived with her father, stepmother and siblings.
Leila's brother was taken into custody at 5:10 p.m. Saturday, and police hastily called a news conference to announce the arrest.
"Citizens of Calaveras County, you can sleep a little better tonight," Kuntz said.
Authorities spent more than 2,000 hours on the investigation "to provide Leila Fowler's family answers to her death," the sheriff said.
Kuntz said the investigation was ongoing and declined to provide further details.
Local officials pledged support Sunday. The Calaveras Unified School District "stands ready to provide whatever level of support and assistance is necessary to the Fowler family" and the community, Superintendent Mark Campbell said in a statement. The district will make counselors available at all schools, he said.
Several days after the killing, hundreds of people gathered at Jenny Lind Elementary School where Leila was a popular third-grader. Her stepmother, Krystal Walters, tearfully thanked the crowd for the support.
"I just want to thank the entire community and all of our family and friends for all the overwhelming amount of support you've given our family," Walters said at the time. "It will never be forgotten. Thank you."