An ex-transport chief had complained that passengers could get lower fares on some routes by taking advice on splitting tickets at booking offices.
George Eckton, a former director of the South East of Scotland Transport Partnership coordinating body, said he hoped it would improve awareness of lower fares.
The Advertising Standards Authority (ASA) told him: “We’ve assessed the ad you highlighted and, from the information we have, we think it likely to have breached the Advertising Codes we administer.”
An ASA spokeswoman said: “Following receipt of this complaint, we assessed the ads in question and wrote to the advertiser to outline the changes they needed to make in accordance with our rules.
“The complainant was concerned the advertiser’s claims on their website for ‘best fare’ and ‘best value’ were potentially misleading as he could book his ticket at a ticket office, split his journey and achieve a cheaper price.
“We offered the advertiser guidance and advice to ensure their advertising complies with the Advertising Codes.
“Taking action of this kind, rather than going down the route of a formal investigation, is an option available to us depending on resources and prioritisation.”
Mr Eckton said: “I welcome the ASA action. I hope it gives all consumers the opportunity to have greater awareness of the best fares, and places the onus on train companies to do more to market in a clear and transparent manner within the difficulties of the current fare structure.
“I am just as an ordinary citizen trying to get a fare system that is fair for all.”
Mr Eckton has also launched a petition at the Scottish Parliament requiring “customers to be given information on the cheapest possible fare as a matter of course”. This would include future ScotRail operators offering an app to show the lowest price option for a trip.
SNP MSP John Mason, co-convener of the Scottish Parliament’s cross-party rail group, called for greater clarity on fares.
He said: “I welcome any improvements to the present system by way of better advertising or the way tickets are sold.
“However, we need to fix the fundamental problem that it should never be cheaper to buy two tickets in place of one.
“No one has explained to me satisfactorily why this is happening.”
A spokesperson for Transport Scotland, which oversees the ScotRail franchise, said: “We thank Mr Eckton for raising this matter and we are aware ScotRail has taken action to resolve it.”
ScotRail said it had been encouraged to amend the wording of its ads to clarify that the prices were the best value offered through its website, as consumers might be able to achieve a cheaper price through other booking means.
Its spokesperson said: “We’re working with the ASA to ensure information on the best value fares on our website and customer communications is clear, concise and not misleading in any way.”