The bamboo was used by his headmaster at Cambridge and County High School for Boys and inspired the cane-wielding character from Floyd's The Wall tour.
The exhibit accompanies a book which logs punishments issued to Waters, now 73, when he was a Cambridge schoolboy.
The book also records beatings for his late band mate Syd Barrett.
Waters has said he felt "inordinately proud" of his own entry for fighting.
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Mr Waters was speaking alongside the band's drummer Nick Mason at a preview of the Pink Floyd exhibition at the V&A in London.
He said he was particularly looking forward to seeing the cane, which he said was used for "flimsy" beatings.
He added that the headmaster "didn't really have his heart" in corporal punishment.
"There's a log of punishment that they [schoolboys] got... six strokes for fighting is my entry which I'm inordinately proud of.
"It's so archaic now, the idea of hitting people with sticks to make them do things."
Mr Mason revealed that Floyd collaborator Storm Thorgerson, who died in 2013, had been the school's most punished pupil, according to the log book.
The show also features a giant replica of the Bedford van the band used as their touring vehicle in the 1960s, while David Gilmour's famous Stratocaster guitar, nicknamed "the black strat", will also be on show.
The exhibition, which starts in May, marks 50 years since the release of the band's first album and their debut single Arnold Layne.
A cane used to beat Pink Floyd's Roger Waters as a schoolboy features among 350 items appearing at an exhibition documenting the band's 50-year history.