The city council has said no extra charge is permitted for wheelchair accessibility.
But undercover filming revealed a woman was told by one cab driver she had to pay more than “normal” people because her wheelchair “was heavy”.
On average, the cost was about two-thirds more for wheelchair users.
A team from Inside Out West Midlands took black-cab journeys across Stoke-on-Trent city centre with Baljeevan Deol, a 22-year-old student, who has generalised dystonia.
The condition means she cannot control her muscles, and she agreed to take part in secretly filming drivers after suspecting she was regularly charged more than her able-bodied friends.
Ms Deol and Inside Out programme production staff made 12 identical trips.
Programme producer Qasa Alom said: “Obviously we are not saying every taxi in Stoke will overcharge, but our investigation found of the 12 journeys we took, Bal was charged more every single time.”
Ms Deol said: “I feel sad and angry. I’m so annoyed this happens and how much money over the last few years I’ve spent extra that I shouldn’t have.
“They can’t get away with this. I feel like I’m being discriminated against and it’s just not fair.”
Abdul Rauf, from the Hackney Carriage Association in Stoke, said drivers breaking the rules should be “brought to book”.
“There is no such thing as an extra charge for wheelchairs, so whoever is doing so is breaking the terms and conditions of their licence.
“We need to identify these guys and bring them before the committee to explain their actions. We in the trade do not condone this; it damages our trade.”
Stoke City Council cabinet member for neighbourhoods, Joy Garner, said drivers’ training included disability awareness, and “they are well aware they shouldn’t be overcharging”.
She also said the council would consider working with disability groups so wheelchair users knew their rights.
“If people use our transport services they should know what to expect and know they don’t have to be ripped off like that.
“It’s saddening; it is a handful bringing rest of the profession into disrepute. It’s really sad,” said Ms Garner.
Inside Out West Midlands is on BBC One at 19:30 on Monday, and afterwards on the iPlayer.