The long-serving Ian Weston will head up the Robins' medical department and act as academy sports therapist.
The hugely respected Bristolian has been with the club since succeeding Andy Mitchell in 2002 and he will also mentor 23-year-old Baker, who worked for the academy last season.
"I can help Joe progress further and I am looking forward to mentoring him and trying to develop the medical department as well," the award winning Weston said.
"A big part of my job will be to try and develop the scholars physically and mentally to try and close the gap between Under-18 and first team football, which should benefit the club in the long term.
"This is a good move for everyone because we have the same personnel, but we need to keep expanding and trying to improve.
"This new role will allow me to do that and I have turned down two job offers for this position because it excites me and I want to be a part of our club and help us get back into the Football League."
Baker is originally from Northampton and he has a BSC in physiotherapy from Coventry University. He worked in the NHS for three years before joining Cheltenham last October, since when he has made a favourable impact with his approach to the job.