Geoff Fisher, head of St Andrew's Church of England primary, said he felt able to leave now that all legal proceedings surrounding the murders of the two 10-year-old girls in August 2002 had finished.
The 55-year-old, who has been head of the Cambridgeshire school for 24 years, will retire at the end of December.
The Rev Tim Alban Jones, the school's vice chair of governors, dismissed reports that Mr Fisher was leaving because he was tormented by the deaths as "poppycock". He said the head had been a tower of strength.
Mr Fisher gave Maxine Carr, the girlfriend of the killer Ian Huntley, a job as a temporary teaching assistant at the primary where she befriended the two pupils. It later emerged she had lied about her qualifications. Mr Fisher said: "My plan had been to leave teaching last year but given the circumstances and timing of the trials of Ian Huntley and Maxine Carr I felt it my duty to see the school through this difficult period.
"Having been in teaching for 35 years I would like to do something different, and I informed school governors and the county council's director of education of my intention to retire at the end of 2004."
At the time of the girls' disappearance Mr Fisher, who lives in Soham, spoke of the "rollercoaster of emotions" faced by local people as initial optimism turned into disbelief and horror. He made it his aim to keep life in his school as normal as possible.
He described the pupils as "two happy, generous, caring, giving little girls" whose memory would live on in the school.
After the murder trial he said the hearings had not provided the answers the town had been looking for. "I think deep down people want to know what went on in there (Huntley's house)," he said.