Elisabeth Cooper, who was in charge of Sudell primary in Darwen, Lancashire, at the time of the incident in 2001, shouted at the boy for five to 10 minutes, a GTCE hearing was told.
The hearing, held in Birmingham on December 18, concluded that Ms Cooper's behaviour was not acceptable for managing young pupils with special needs.
Her reprimand will remain on the GTCE register for two years.
Anthony Cuthbert, committee chairman, said: "Ms Cooper's treatment of the child was reprehensible, and involved a wholesale departure from accepted standards of teaching practice concerning the behaviour management of young pupils with special educational needs."
At an earlier hearing in November, Ivy Pollard, school secretary, described the head's behaviour as "disturbing".
She said: "I was concerned when it got to screaming pitch that something could happen to the child or her."
Geoff Tennant, the former head of a neighbouring school who was acting as a mentor to Ms Cooper, told the GTCE that he noticed the boy seemed extremely frightened after the incident.
He said: "He told me he expected to be really shouted at and when I asked why he said 'Ms Cooper did a lot of shouting'."
Ms Cooper, who was not present at the hearing, was also accused of unacceptable professional conduct for leaving pupils who had arrived late to stand in her office for up to 45 minutes without supervision.
Mrs Pollard said: "She would slam the door with such a considerable force that it made me jump.
"There could be up to six children of all ages there at a time and the reception-aged children seemed scared. They did not understand what was happening to them."
The GTCE decided that, although this practice was misguided, it did not breach standards expected in the profession.
Further allegations of bullying by Ms Cooper towards other staff members, including inappropriate remarks and shouting, amounted to undesirable management but did not breach standards, the panel found.
Linda Wallis, a learning support assistant, broke down in tears when she told the earlier hearing: "She kept telling me to shut up and said 'I don't want to see your face around school, you better keep out of my way'."
The committee concluded that, although she was a capable teacher and deputy head, Ms Cooper was working at or beyond the limit of her capabilities at that time.
They also recognised that she was under stress, and trying to cope with the school being rebuilt.