More than a 10th of children needing routine treatment at Bedfordshire Hospitals Trust in May had been waiting too long, figures show, with some waiting more than a year.
Families can feel as though they are in "limbo", while long waiting lists and difficulties accessing timely care could put children's development at risk, experts say.
NHS rules state patients referred for non-urgent consultant-led care should be seen within 18 weeks.
But data from NHS Digital shows 16 per cent of patients on the waiting list for paediatric care at Bedfordshire Hospitals NHS Foundation Trust in May had been waiting longer.
It means 368 children waited longer than the target time.
Among those were 84 who had been waiting more than 36 weeks, at least double the recommended time.
And despite a "zero tolerance" approach to waits of more than 52 weeks, 40 children in the area had been on the waiting list for a year.
Bedford Today approached Bedfordshire Hospitals Trust for comment earlier this week.
Across England, more than 72,600 youngsters had been on the waiting list for more than 18 weeks in May, meaning around 29 per cent had been waiting too long for treatment.
Nationally, paediatric patients are generally seen faster than those waiting for general surgery, but the figures show a larger proportion of children were facing long waits than the elderly or mentally ill in May.
The Patients Association and Healthwatch England have called on the NHS to ensure families are kept up to date while waiting for treatment.
Chris McCann of Healthwatch said it was worrying to see that more than a quarter of children on NHS waiting lists had been awaiting treatment for more than 18 weeks.
He said the coronavirus pandemic has resulted in more patients feeling "stressed, confused and ignored" over changes to their healthcare, adding: "If some children who have underlying health conditions don’t receive timely care, this may affect their long-term development and wellbeing.
"With appointments having been cancelled last year and the NHS facing a backlog, those affected also need to be informed where they are on a waiting list."
Patient Association chief executive Rachel Power, said a long wait could have an impact on whether a parent can work, adding: “Waiting for a child to receive treatment can be a very worrying time for families, especially if a child is in discomfort or even pain.
"Some families are sure to feel they’re in some kind of limbo."
The NHS figures show the number of people waiting longer than 18 weeks or a year across all treatment areas nationally fell significantly between May 2020 and May this year.
However, there is no comparable data available for paediatric treatment waiting times prior to the beginning of the 2021 financial year.
Commenting on the wider figures, NHS Medical Director Professor Stephen Powis said: “Despite the huge disruption we have seen to care caused by the pandemic and the more than 405,000 Covid patients in our hospitals over the last 15 months, it is reassuring to see significant reductions in waits for routine operations and a reduction in the number of patients waiting more than 18 weeks for treatment."