The now-17-year-old girl was just 68 pounds when she fled the family's home in February 2012. She told doctors her parents kept her in the basement with boarded up windows, motion sensors and an alarm on the basement door.
Prosecutors said the man sexually assaulted the girl starting from when she was 9 years old because he thought he could get away with it. The Associated Press isn't naming the man to avoid identifying the girl.
The judge's secretary said Friday that jurors delivered their verdict around midnight after deliberating for roughly 10 hours on the charges of first-degree sexual assault of a child, second-degree sexual assault of a child and child abuse. They convicted the man on all charges.
Prosecutors said the abuse happened between 2006 and 2011 in the home where the then-children lived with the girl's father and the boy's mother.
Defense attorney Ronald Benavides didn't immediately respond to requests for comment.
Judge Julie Genovese scheduled sentencing for Wednesday. She could also sentence him then in another sexual assault case from December 2012. That case also involved a child.
The man pleaded no contest to sexual assault charges in a separate case in November 2011 and served 15 months in prison in that case.
Benavides argued that there were inconsistencies in the stepsister's story that should prevent jurors from believing her accusations. A school social worker became involved after the girl said something at her elementary school that led officials to believe she may have been being abused at home. The girl later told the social worker she wasn't actually sexually abused.
There was also a lack of physical evidence for the sexual assault charges, as doctors who examined the girl in 2012 said there was no evidence of sexual assault.
Assistant Dane County District Attorney Matt Moeser told jurors that the girl's father and stepmother put her into in-patient psychiatric care after she told them about the first sexual assault.
Moeser said the parents' punishment of the girl, along with her mistreatment, may have explained her reluctance to tell authorities she had been sexually assaulted in the home. He called living conditions there a "perfect storm" for sexual abuse.
The parents were convicted and sentenced to five years each in prison in separate trials.