In six months, the gap between the most expensive and cheapest tariffs had widened by up to a third.
The charity explained that Co-operative Energy, that held the largest gap of £405, replied to the report saying it will cut its pre-payment rates.
This report comes ahead of an inquiry into the entire energy industry.
The investigation which is being carried out by The Competition and Markets Authority (CMA) started a year ago, and will report its findings on Tuesday 7 July.
The chief executive of Citizens Advice, Gillian Guy, said: “The CMA investigation provides an opportunity to overhaul the energy industry and make it fairer,”
“Giving pre-payment meter customers a better deal is a crucial part of this.”
According to research, those who are using the pre-payment option are more likely to be on a low income, and around 80% of those getting the systems installed are already in debt. If their supplier gains a court order, those who fall behind with payments will be forced to have them installed.
Users of the service pay for their gas and electricity by topping up cards, paying in advance or by buying tokens.
The most extreme difference is held by Co-operative Energy. A customer would have to pay £1,356 if they were using a pre-payment meter, but only £951 a year if they were on the company’s cheapest direct debit plan – a difference of £405.
Co-operative Energy said: “Following contact with Citizens Advice, we have taken the opportunity to review our dual fuel pre-payment tariff and will be reducing it to match the cheapest of the Big Six rates immediately.”