David Doubtfire has stepped down from his position at Walkwood Middle School in Redditch.
The 51-year-old, of Bidford-on-Avon, is due to appear at Worcester Magistrates' Court on Friday.
The voyeurism charge relates to an alleged incident at Evesham Leisure Centre. Mr Doubtfire is currently on police bail.
A statement on Walkwood Middle School's website said the charges were "unrelated to children or his former role at the school".
It added: "Mr Doubtfire has not been at Walkwood since we were informed about the police investigation and formally resigned as head when the charges were brought.
"We are unable to comment further while the court process is ongoing."
A former head teacher has been charged with voyeurism and three counts of possessing extreme pornography.