Mott led the team for 11 years.
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Currently, all eight JV football players face accusation in an alleged hazing incident that occurred last October.
RELATED: Police investigate alleged assaults involving Napa football team
The Napa Valley Register reports that Mott's departure came after what he described as varying philosophies on the program's future.
Napa Valley Unified School District held a public expulsion hearing Tuesday for a football player accused of hazing.
The hearing was held to decide whether or not to expel Johnny Torres, a Napa High School JV football player, for one year.
"I am here because I am concerned there should be a fair process," said Rachel Smith, a parent.
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RELATED: Napa parents frustrated by high school football hazing investigation
Torres along with eight other JV football players is facing expulsion after an alleged hazing incident.
According to a declaration by one player, they charged and held another player down while a third poked that player through his uniform pants, in the rear end.
Torres says it was just horseplay. "When kids are in a locker room horse playing, that may be obnoxious and annoying, but that is not sexual," said Torres' attorney.
A student told an administrator, who was required by state law to report it to police, who now continue to investigate.
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RELATED: Police say Napa football assaults may be ritual hazing
In the meantime, Johnny Torres, who had been an honor student, has been out of school for 10-weeks, and worries about his future.
The school board could vote on Torres as early as Wednesday night.
Watch ABC7 News at 6 p.m. for more on this developing story.
ABC7 News's Wayne Freedman contributed to this story.