Northern contacted Mr Williamson, 22, on Friday to inform him his case would be closed after his story was picked up from social media.
The publicly owned company has now confirmed it will also review up to 25 historical cases it had prosecuted since 2020.
The operator said it was working with the government to “simplify its price structure”.
“We understand that fares and ticketing across the railway can, at times, be difficult to understand, and we are reviewing our processes for ensuring compliance with ticket and railcard terms and conditions,” a statement read.
“With regard to recent reported cases involving use of the 16-25 railcard with fares under £12 before 10am, we are withdrawing any live cases and will also look to review anyone who has been prosecuted previously on this specific issue.
“We are actively engaged with the government and industry to simplify fares to help customers.
“We have withdrawn two cases today and two more are to be withdrawn at the end of the month that are already in the system.
“We will ensure that anything coming up for review does not go forward for prosecution.”