The original study of 44 children, who all took the controversial drugs for a year or more, found no mental health impact - neither benefits nor harm.
But a re-analysis of that data now suggests 34% saw their mental health deteriorate, while 29% improved.
The authors of the original report have welcomed the new evidence.
The re-analysis, which has been seen by BBC Newsnight, questions some of the conclusions from the 2021 study about the potential mental health impact of puberty blockers on under 16s. It also sheds some light on this much-debated, but little understood, area of children's medicine.
The new study has not been in a peer-reviewed journal yet. The authors say they felt there was an urgency in getting the information into the public domain.
The study is small - just 44 young people. And because of the way the original study was designed - without a control group - experts can't infer cause and effect or say these changes in wellbeing were caused by being on puberty blockers.
But despite those limitations, the new analysis suggests the need for more research, both into this specific group and on the impact of puberty blockers more generally.
Children on puberty blockers saw mental health change - new analysis - BBC News
(Presumably this will be a newsnight report - maybe tonight or later in the week?)