Demin Zawity, 14, said she felt like crying when her commanding officers told her she couldn't wear the head covering with her uniform.
"They were making something that is not such a huge deal into something so dramatic," she said. "The next day was the parade, and I couldn't march."
Carol Birdsong, a school spokeswoman, said the district follows military regulations for the U.S. Army program.
Zawity's mother, Perishan Hussein, said she contacted the Council on American-Islamic Relations about her daughter's treatment.
"There are some Muslims who say she shouldn't be involved in this, and there will be Americans who say she needs to assimilate," Hussein said. "She's an American. I'm an American. She has a right to stand up for her rights."
Zawity has since quit the JROTC and returned to regular physical education classes, but she said she wants to make it easier for Muslim girls to participate in the future.
A New Jersey teen dropped out of the Naval Junior ROTC in 2003 over the same issue. Her school ultimately offered to exempt her from the uniform rules.
Fremont, with weekly attendance of about 1,400, is the seventh Sacramento-area church to leave the mainline Presbyterian Church over doctrinal issues in the past few years.
About 800 Fremont congregants attended the meeting about the pros and cons of what is technically known as seeking "dismissal" from the mainline Presbyterian fold. Supporters of the separation argued that their denomination had drifted away from biblical teachings with its decision to allow gay ministers.
Scott Anderson became the denomination's first openly gay minister when he was reordained last week in Wisconsin. He served as a Presbyterian minister in Sacramento for seven years before he came out to his congregation and resigned in 1990.
"This is a day of rejoicing. It frees us from the controversy that has split the church," said Clair Parsh, a member for 50 years who favored leaving the denomination.
Cindy Harris, who is preparing to become a minister herself, resisted the change and wiped away tears after the vote.
"I think God can and will call whoever he wants to call, regardless of sex or orientation," she said, wiping away tears after the vote.