Richard Evans initially was charged for one alleged incident on Nov. 3, but prosecutors added more charges Monday after learning about a second.
He was charged with two more counts of sexual assault of a child under 10, and another charge of lewd and lascivious acts with a child under 14.
Reed said the second reported incident occurred in late October, two weeks prior to the first reported incident on Nov. 2.
The 59-year-old is a former full-time driver for Lodi Unified School District who returned as a substitute driver in 2008.
Prosecutors say Evans picked up the girl from home and molested her before picking up other students.
She later told her parents.
Evans has not yet entered a plea, and his attorney has requested a gag order in the case.
He's being held on $2.4 million bail.